WorldWideScience

Sample records for dynamic molecular imaging

  1. Dynamic fluorescence imaging with molecular agents for cancer detection

    Science.gov (United States)

    Kwon, Sun Kuk

    Non-invasive dynamic optical imaging of small animals requires the development of a novel fluorescence imaging modality. Herein, fluorescence imaging is demonstrated with sub-second camera integration times using agents specifically targeted to disease markers, enabling rapid detection of cancerous regions. The continuous-wave fluorescence imaging acquires data with an intensified or an electron-multiplying charge-coupled device. The work presented in this dissertation (i) assessed dose-dependent uptake using dynamic fluorescence imaging and pharmacokinetic (PK) models, (ii) evaluated disease marker availability in two different xenograft tumors, (iii) compared the impact of autofluorescence in fluorescence imaging of near-infrared (NIR) vs. red light excitable fluorescent contrast agents, (iv) demonstrated dual-wavelength fluorescence imaging of angiogenic vessels and lymphatics associated with a xenograft tumor model, and (v) examined dynamic multi-wavelength, whole-body fluorescence imaging with two different fluorescent contrast agents. PK analysis showed that the uptake of Cy5.5-c(KRGDf) in xenograft tumor regions linearly increased with doses of Cy5.5-c(KRGDf) up to 1.5 nmol/mouse. Above 1.5 nmol/mouse, the uptake did not increase with doses, suggesting receptor saturation. Target to background ratio (TBR) and PK analysis for two different tumor cell lines showed that while Kaposi's sarcoma (KS1767) exhibited early and rapid uptake of Cy5.5-c(KRGDf), human melanoma tumors (M21) had non-significant TBR differences and early uptake rates similar to the contralateral normal tissue regions. The differences may be due to different compartment location of the target. A comparison of fluorescence imaging with NIR vs. red light excitable fluorescent dyes demonstrates that NIR dyes are associated with less background signal, enabling rapid tumor detection. In contrast, animals injected with red light excitable fluorescent dyes showed high autofluorescence. Dual

  2. Towards imaging of ultrafast molecular dynamics using FELs

    NARCIS (Netherlands)

    Rouzee, A.; Johnsson, P.; Rading, L.; Siu, W.; Huismans, Y.; Duesterer, S.; Redlin, H.; Tavella, F.; Stojanovic, N.; Al-Shemmary, A.; Lepine, F.; Holland, D. M. P.; Schlathölter, Thomas; Hoekstra, R.; Fukuzawa, H.; Ueda, K.; Vrakking, M. J. J.; Hundertmark, A.

    2013-01-01

    The dissociation dynamics induced by a 100 fs, 400 nm laser pulse in a rotationally cold Br-2 sample was characterized by Coulomb explosion imaging (CEI) using a time-delayed extreme ultra-violet (XUV) FEL pulse, obtained from the Free electron LASer in Hamburg (FLASH). The momentum distribution of

  3. Dynamical image-charge effect in molecular tunnel junctions

    DEFF Research Database (Denmark)

    Jin, Chengjun; Thygesen, Kristian Sommer

    2014-01-01

    the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z(2), where Z is the quasiparticle renormalization factor, compared to the static IC approximation...... that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels....

  4. Investigating Atmospheric Oxidation with Molecular Dynamics Imaging and Spectroscopy

    Science.gov (United States)

    Merrill, W. G.; Case, A. S.; Keutsch, F. N.

    2013-06-01

    Volatile organic compounds (VOCs) in the Earth's atmosphere constitute trace gas species emitted primarily from the biosphere, and are the subject of inquiry for a variety of air quality and climate studies. Reactions intiated (primarily) by the hydroxyl radical (OH) lead to a myriad of oxygenated species (OVOCs), which in turn are prone to further oxidation. Investigations of the role that VOC oxidation plays in tropospheric chemistry have brought to light two troubling scenarios: (1) VOCs are responsible in part for the production of two EPA-regulated pollutants---tropospheric ozone and organic aerosol---and (2) the mechanistic details of VOC oxidation remain convoluted and poorly understood. The latter issue hampers the implementation of near-explicit atmospheric simulations, and large discrepancies in OH reactivity exist between measurements and models at present. Such discrepancies underscore the need for a more thorough description of VOC oxidation. Time-of-flight measurements and ion-imaging techniques are viable options for resolving some of the mechanistic and energetic details of VOC oxidation. Molecular beam studies have the advantage of foregoing unwanted bimolecular reactions, allowing for the characterization of specific processes which must typically compete with the complex manifold of VOC oxidation pathways. The focus of this work is on the unimolecular channels of organic peroxy radical intermediates, which are necessarily generated during VOC oxidation. Such intermediates may isomerize and decompose into distinct chemical channels, enabling the unambiguous detection of each pathway. For instance, a (1 + 1') resonance enhanced multiphoton ionization (REMPI) scheme may be employed to detect carbon monoxide generated from a particular unimolecular process. A number of more subtle mechanistic details may be explored as well. By varying the mean free path of the peroxy radicals in a flow tube, the role of collisional quenching in these unimolecular

  5. Identification of a Common Binding Mode for Imaging Agents to Amyloid Fibrils from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Skeby, Katrine Kirkeby; Sørensen, Jesper; Schiøtt, Birgit

    2013-01-01

    experimentally due to the insoluble nature of amyloid fibrils. This study uses molecular dynamics simulations to investigate the interactions between 13 aromatic amyloid imaging agents, entailing 4 different organic scaffolds, and a model of an amyloid fibril. Clustering analysis combined with free energy...

  6. Imaging Multi-Particle Atomic and Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Landers, Allen [Auburn Univ., AL (United States)

    2016-02-12

    Final Report for Grant Number: DE- FG02-10ER16146 This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms and molecules with photons and electrons. The duration of the grant was the 5 year period from 4/1/2010 – 10/31/2015. All of the support from the grant was used to pay salaries of the PI, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 20 peer reviewed publications over these 5 years with 2 of the publications in Physical Review Letters and 1 in Nature; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B ...).

  7. Facilitating in vivo tumor localization by principal component analysis based on dynamic fluorescence molecular imaging

    Science.gov (United States)

    Gao, Yang; Chen, Maomao; Wu, Junyu; Zhou, Yuan; Cai, Chuangjian; Wang, Daliang; Luo, Jianwen

    2017-09-01

    Fluorescence molecular imaging has been used to target tumors in mice with xenograft tumors. However, tumor imaging is largely distorted by the aggregation of fluorescent probes in the liver. A principal component analysis (PCA)-based strategy was applied on the in vivo dynamic fluorescence imaging results of three mice with xenograft tumors to facilitate tumor imaging, with the help of a tumor-specific fluorescent probe. Tumor-relevant features were extracted from the original images by PCA and represented by the principal component (PC) maps. The second principal component (PC2) map represented the tumor-related features, and the first principal component (PC1) map retained the original pharmacokinetic profiles, especially of the liver. The distribution patterns of the PC2 map of the tumor-bearing mice were in good agreement with the actual tumor location. The tumor-to-liver ratio and contrast-to-noise ratio were significantly higher on the PC2 map than on the original images, thus distinguishing the tumor from its nearby fluorescence noise of liver. The results suggest that the PC2 map could serve as a bioimaging marker to facilitate in vivo tumor localization, and dynamic fluorescence molecular imaging with PCA could be a valuable tool for future studies of in vivo tumor metabolism and progression.

  8. Full-direct method for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guanglei, E-mail: guangleizhang@bjtu.edu.cn [Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084 (China); Department of Biomedical Engineering, School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044 (China); Pu, Huangsheng; Liu, Fei; Bai, Jing [Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084 (China); He, Wei [China Institute of Sport Science, Beijing 100061 (China); Luo, Jianwen, E-mail: luo-jianwen@tsinghua.edu.cn [Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084 (China); Center for Biomedical Imaging Research, School of Medicine, Tsinghua University, Beijing 100084 (China)

    2015-02-23

    Images of pharmacokinetic parameters (also known as parametric images) in dynamic fluorescence molecular tomography (FMT) can provide three-dimensional metabolic information for biological studies and drug development. However, the ill-posed nature of FMT and the high temporal variation of fluorophore concentration together make it difficult to obtain accurate parametric images in small animals in vivo. In this letter, we present a method to directly reconstruct the parametric images from the boundary measurements based on hybrid FMT/X-ray computed tomography (XCT) system. This method can not only utilize structural priors obtained from the XCT system to mitigate the ill-posedness of FMT but also make full use of the temporal correlations of boundary measurements to model the high temporal variation of fluorophore concentration. The results of numerical simulation and mouse experiment demonstrate that the proposed method leads to significant improvements in the reconstruction quality of parametric images.

  9. Tracking molecular dynamics without tracking: image correlation of photo-activation microscopy

    International Nuclear Information System (INIS)

    Pandžić, Elvis; Rossy, Jérémie; Gaus, Katharina

    2015-01-01

    Measuring protein dynamics in the plasma membrane can provide insights into the mechanisms of receptor signaling and other cellular functions. To quantify protein dynamics on the single molecule level over the entire cell surface, sophisticated approaches such as single particle tracking (SPT), photo-activation localization microscopy (PALM) and fluctuation-based analysis have been developed. However, analyzing molecular dynamics of fluorescent particles with intermittent excitation and low signal-to-noise ratio present at high densities has remained a challenge. We overcame this problem by applying spatio-temporal image correlation spectroscopy (STICS) analysis to photo-activated (PA) microscopy time series. In order to determine under which imaging conditions this approach is valid, we simulated PA images of diffusing particles in a homogeneous environment and varied photo-activation, reversible blinking and irreversible photo-bleaching rates. Further, we simulated data with high particle densities that populated mobile objects (such as adhesions and vesicles) that often interfere with STICS and fluctuation-based analysis. We demonstrated in experimental measurements that the diffusion coefficient of the epidermal growth factor receptor (EGFR) fused to PAGFP in live COS-7 cells can be determined in the plasma membrane and revealed differences in the time-dependent diffusion maps between wild-type and mutant Lck in activated T cells. In summary, we have developed a new analysis approach for live cell photo-activation microscopy data based on image correlation spectroscopy to quantify the spatio-temporal dynamics of single proteins. (paper)

  10. Tracking molecular dynamics without tracking: image correlation of photo-activation microscopy

    Science.gov (United States)

    Pandžić, Elvis; Rossy, Jérémie; Gaus, Katharina

    2015-03-01

    Measuring protein dynamics in the plasma membrane can provide insights into the mechanisms of receptor signaling and other cellular functions. To quantify protein dynamics on the single molecule level over the entire cell surface, sophisticated approaches such as single particle tracking (SPT), photo-activation localization microscopy (PALM) and fluctuation-based analysis have been developed. However, analyzing molecular dynamics of fluorescent particles with intermittent excitation and low signal-to-noise ratio present at high densities has remained a challenge. We overcame this problem by applying spatio-temporal image correlation spectroscopy (STICS) analysis to photo-activated (PA) microscopy time series. In order to determine under which imaging conditions this approach is valid, we simulated PA images of diffusing particles in a homogeneous environment and varied photo-activation, reversible blinking and irreversible photo-bleaching rates. Further, we simulated data with high particle densities that populated mobile objects (such as adhesions and vesicles) that often interfere with STICS and fluctuation-based analysis. We demonstrated in experimental measurements that the diffusion coefficient of the epidermal growth factor receptor (EGFR) fused to PAGFP in live COS-7 cells can be determined in the plasma membrane and revealed differences in the time-dependent diffusion maps between wild-type and mutant Lck in activated T cells. In summary, we have developed a new analysis approach for live cell photo-activation microscopy data based on image correlation spectroscopy to quantify the spatio-temporal dynamics of single proteins.

  11. Progress on molecular imaging

    International Nuclear Information System (INIS)

    Chen Quan; Zhang Yongxue

    2011-01-01

    Molecular imaging is a new era of medical imaging,which can non-invasively monitor biological processes at the cellular and molecular level in vivo, including molecular imaging of nuclear medicine, magnetic resonance molecular imaging, ultrasound molecular imaging,optical molecular imaging and molecular imaging with X-ray. Recently, with the development of multi-subjects amalgamation, multimodal molecular imaging technology has been applied in clinical imaging, such as PET-CT and PET-MRI. We believe that with development of molecular probe and multi-modal imaging, more and more molecular imaging techniques will be applied in clinical diagnosis and treatment. (authors)

  12. Molecular imaging of in vivo redox dynamics using magnetic resonance system

    International Nuclear Information System (INIS)

    Utsumi, Hideo; Yasukawa, Keiji

    2008-01-01

    Homeostatic failure through redox systems in vivo results in abnormality in mitochondrial function, protein expression and metabolism leading to many diseases like lifestyle related ones and cancer. It is therefore important to see redox dynamics for early prevention of the diseases. This paper describes development of machines for electron spin resonance (ESR) imaging of the redox state, for Overhauser Effect MRI (OMRI), application of nitroxyl-probes and state of redox project by authors. They have developed the ESR equipments hitherto, including the latest 300 MHz one, with which images of a mouse given carbamoyl-PROXYL probe are obtained and fused with MRI images for anatomical positioning: resonator for both ESR and MRI coils has been developed for animal images. Philips OMRI machine has been able to give separate images of reduction and oxidation in animals given appropriate probe compounds, which lead to molecular imaging of redox using such probes as 14 N- and 15 N-nitroxyl radicals with different membrane permeability. Application of nitroxyl-radicals like hydroxyl-TEMPO has made it possible for the animal diseases caused by oxidative stress to be analyzed by ESR/spin probe method, and derivatization of the probe results in detection of its distribution in various cell and body areas even in nanometer-space. Authors' project concerns the development of the processing system of redox dynamics/OMRI-integrated images, of better probe complexes and application of these to actual model animals. The techniques are thought to be important in the fields of medicare and new drug development in future. (R.T.)

  13. Photoelectron photoion coincidence imaging of ultrafast control in multichannel molecular dynamics.

    Science.gov (United States)

    Lehmann, C Stefan; Ram, N Bhargava; Irimia, Daniel; Janssen, Maurice H M

    2011-01-01

    The control of multichannel ionic fragmentation dynamics in CF3I is studied by femtosecond pulse shaping and velocity map photoelectron photoion coincidence imaging. When CF3I is photoexcited with femtosecond laser pulses around 540 nm there are two major ions observed in the time-of-flight mass spectrum, the parent CF3I+ ion and the CF3+ fragment ion. In this first study we focussed on the influence of LCD-shaped laser pulses on the molecular dynamics. The three-dimensional recoil distribution of electrons and ions were imaged in coincidence using a single time-of-flight delay line detector. By fast switching of the voltages on the various velocity map ion lenses after detection of the electron, both the electron and the coincident ion are measured with the same imaging detector. These results demonstrate that a significant simplification of a photoelectron-photoion coincidence imaging apparatus is in principle possible using switched lens voltages. It is observed that shaped laser fields like chirped pulses, double pulses, and multiple pulses can enhance the CF3+CF3I+ ratio by up to 100%. The total energetics of the dynamics is revealed by analysis of the coincident photoelectron spectra and the kinetic energy of the CF3+ and I fragments. Both the parent CF3I+ and the CF3+ fragment result from a five-photon excitation process. The fragments are formed with very low kinetic energy. The photoelectron spectra and CF3+/CF3I+ ratio vary with the center wavelength of the shaped laser pulses. An optimal enhancement of the CF3+/CF3I+ ratio by about 60% is observed for the double pulse excitation when the pulses are spaced 60 fs apart. We propose that the control mechanism is determined by dynamics on neutral excited states and we discuss the results in relation to the location of electronically excited (Rydberg) states of CF3I.

  14. EDITORIAL: Molecular Imaging Technology

    Science.gov (United States)

    Asai, Keisuke; Okamoto, Koji

    2006-06-01

    'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

  15. Correlating TEM images of damage in irradiated materials to molecular dynamics simulations

    International Nuclear Information System (INIS)

    Schaeublin, R.; Caturla, M.-J.; Wall, M.; Felter, T.; Fluss, M.; Wirth, B.D.; Diaz de la Rubia, T.; Victoria, M.

    2002-01-01

    TEM image simulations are used to couple the results from molecular dynamics (MD) simulations to experimental TEM images. In particular we apply this methodology to the study of defects produced during irradiation. MD simulations have shown that irradiation of FCC metals results in a population of vacancies and interstitials forming clusters. The limitation of these simulations is the short time scales available, on the order of 100 s of picoseconds. Extrapolation of the results from these short times to the time scales of the laboratory has been difficult. We address this problem by two methods: we perform TEM image simulations of MD simulations of cascades with an improved technique, to relate defects produced at short time scales with those observed experimentally at much longer time scales. On the other hand we perform in situ TEM experiments of Au irradiated at liquid-nitrogen temperatures, and study the evolution of the produced damage as the temperature is increased to room temperature. We find that some of the defects observed in the MD simulations at short time scales using the TEM image simulation technique have features that resemble those observed in laboratory TEM images of irradiated samples. In situ TEM shows that stacking fault tetrahedra are present at the lowest temperatures and are stable during annealing up to room temperature, while other defect clusters migrate one dimensionally above -100 deg. C. Results are presented here

  16. Molecular MR Imaging Probes

    OpenAIRE

    MAHMOOD, UMAR; JOSEPHSON, LEE

    2005-01-01

    Magnetic resonance imaging (MRI) has been successfully applied to many of the applications of molecular imaging. This review discusses by example some of the advances in areas such as multimodality MR-optical agents, receptor imaging, apoptosis imaging, angiogenesis imaging, noninvasive cell tracking, and imaging of MR marker genes.

  17. Targeted molecular imaging

    International Nuclear Information System (INIS)

    Kim, E. Edmund

    2003-01-01

    Molecular imaging aims to visualize the cellular and molecular processes occurring in living tissues, and for the imaging of specific molecules in vivo, the development of reporter probes and dedicated imaging equipment is most important. Reporter genes can be used to monitor the delivery and magnitude of therapeutic gene transfer, and the time variation involved. Imaging technologies such as micro-PET, SPECT, MRI and CT, as well as optical imaging systems, are able to non-invasively detect, measure, and report the simultaneous expression of multiple meaningful genes. It is believed that recent advances in reporter probes, imaging technologies and gene transfer strategies will enhance the effectiveness of gene therapy trials

  18. Spatio-temporal image correlation spectroscopy and super-resolution microscopy to quantify molecular dynamics in T cells.

    Science.gov (United States)

    Ashdown, George W; Owen, Dylan M

    2018-02-02

    Many cellular processes are regulated by the spatio-temporal organisation of signalling complexes, cytoskeletal components and membranes. One such example is at the T cell immunological synapse where the retrograde flow of cortical filamentous (F)-actin from the synapse periphery drives signalling protein microclusters towards the synapse centre. The density of this mesh however, makes visualisation and analysis of individual actin fibres difficult due to the resolution limit of conventional microscopy. Recently, super-resolution methods such as structured illumination microscopy (SIM) have surpassed this resolution limit. Here, we apply SIM to better visualise the dense cortical actin meshwork in T cell synapses formed against activating, antibody-coated surfaces and image under total-internal reflection fluorescence (TIRF) illumination. To analyse the observed molecular flows, and the relationship between them, we apply spatio-temporal image correlation spectroscopy (STICS) and its cross-correlation variant (STICCS). We show that the dynamic cortical actin mesh can be visualised with unprecedented detail and that STICS/STICCS can output accurate, quantitative maps of molecular flow velocity and directionality from such data. We find that the actin flow can be disrupted using small molecule inhibitors of actin polymerisation. This combination of imaging and quantitative analysis may provide an important new tool for researchers to investigate the molecular dynamics at cellular length scales. Here we demonstrate the retrograde flow of F-actin which may be important for the clustering and dynamics of key signalling proteins within the plasma membrane, a phenomenon which is vital to correct T cell activation and therefore the mounting of an effective immune response. Copyright © 2018. Published by Elsevier Inc.

  19. The design and performance of a velocity map imaging spectrometer for the study of molecular photoionisation dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Holland, D.M.P., E-mail: david.holland@stfc.ac.uk [Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD (United Kingdom); Shaw, D.A. [Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD (United Kingdom)

    2012-12-10

    Highlights: Black-Right-Pointing-Pointer Velocity map imaging spectrometer optimised for molecular photoionisation dynamics. Black-Right-Pointing-Pointer Kinetic energy distribution of O{sup +} fragments measured. Black-Right-Pointing-Pointer Effect of autoionisation on photoelectron vibrational populations studied. -- Abstract: The design, construction and performance of a velocity map imaging spectrometer for the study of molecular photoionisation dynamics is described. The spectrometer has been optimised for the efficient collection and detection of particles (electrons or positively charged ions) generated through the interaction of gas phase molecules with synchrotron radiation. A double Einzel lens, incorporated into the flight tube, enhances the collection efficiency of energetic particles. Computer modelling has been used to trace the trajectories of charged particles through the spectrometer and to assess the image quality. A time and position sensitive delay-line detector is used to record the images. Results from two experimental studies are presented to illustrate the capabilities of the spectrometer. In the first, the effect of electronic autoionisation on the vibrationally resolved photoelectron branching ratios of the N{sub 2}{sup +} X {sup 2}{Sigma}{sub g}{sup +} state has been investigated in an excitation range where prominent structure due to Rydberg states occurs in the ion yield curve. The results show that autoionisation leads to rotational branch populations that differ from those observed in direct, non-resonant, photoionisation. In the second, the kinetic energy distribution and the angular distribution of O{sup +} fragments formed in the dissociative photoionisation of molecular oxygen have been measured. The timing properties of the detector have allowed O{sup +} fragments to be separated from O{sub 2}{sup +} parent ions using time-of-flight techniques.

  20. Molecular imaging in oncology

    Energy Technology Data Exchange (ETDEWEB)

    Schober, Otmar; Riemann, Burkhard (eds.) [Universitaetsklinikum Muenster (Germany). Klinik fuer Nuklearmedizin

    2013-02-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  1. Molecular imaging in oncology

    International Nuclear Information System (INIS)

    Schober, Otmar; Riemann, Burkhard

    2013-01-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  2. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  3. Nanoplatform-based molecular imaging

    National Research Council Canada - National Science Library

    Chen, Xiaoyuan

    2011-01-01

    "Nanoplathform-Based Molecular Imaging provides rationale for using nanoparticle-based probes for molecular imaging, then discusses general strategies for this underutilized, yet promising, technology...

  4. Cardiovascular Molecular Imaging

    International Nuclear Information System (INIS)

    Lee, Kyung Han

    2009-01-01

    Molecular imaging strives to visualize processes in living subjects at the molecular level. Monitoring biochemical processes at this level will allow us to directly track biological processes and signaling events that lead to pathophysiological abnormalities, and help make personalized medicine a reality by allowing evaluation of therapeutic efficacies on an individual basis. Although most molecular imaging techniques emerged from the field of oncology, they have now gradually gained acceptance by the cardiovascular community. Hence, the availability of dedicated high-resolution small animal imaging systems and specific targeting imaging probes is now enhancing our understanding of cardiovascular diseases and expediting the development of newer therapies. Examples include imaging approaches to evaluate and track the progress of recent genetic and cellular therapies for treatment of myocardial ischemia. Other areas include in vivo monitoring of such key molecular processes as angiogenesis and apoptosis. Cardiovascular molecular imaging is already an important research tool in preclinical experiments. The challenge that lies ahead is to implement these techniques into the clinics so that they may help fulfill the promise of molecular therapies and personalized medicine, as well as to resolve disappointments and controversies surrounding the field

  5. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  6. Molecular cardiovascular imaging

    International Nuclear Information System (INIS)

    Schaefers, M.

    2007-01-01

    Although huge and long-lasting research efforts have been spent on the development of new diagnostic techniques investigating cardiovascular diseases, still fundamental challenges exist; the main challenge being the diagnosis of a suspected or known coronary artery disease or its consequences (myocardial infarction, heart failure etc.). Beside morphological techniques, functional imaging modalities are available in clinical diagnostic algorithms, whereas molecular cardiovascular imaging techniques are still under development. This review summarizes clinical-diagnostical challenges of modern cardiovascular medicine as well as the potential of new molecular imaging techniques to face these. (orig.)

  7. Molecular dynamics for fermions

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    2000-02-01

    The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

  8. Molecular imaging in oncology

    International Nuclear Information System (INIS)

    Weber, W.A.

    2007-01-01

    Molecular imaging is generally defined as noninvasive and quantitative imaging of targeted macromolecules and biological processes in living organisms. A characteristic of molecular imaging is the ability to perform repeated studies and assess changes in biological processes over time. Thus molecular imaging lends itself well for monitoring the effectiveness of tumor therapy. In animal models a variety of techniques can be used for molecular imaging. These include optical imaging (bioluminescence and fluorescence imaging), magnetic resonance imaging (MRI) and nuclear medicine techniques. In the clinical setting, however, nuclear medicine techniques predominate, because so far only radioactive tracers provide the necessary sensitivity to study expression and function of macromolecules non-invasively in patients. Nuclear medicine techniques allows to study a variety of biological processes in patients. These include the expression of various receptors (estrogen, androgen, somatostatin receptors and integrins). In addition, tracers are available to study tumor cell proliferation and hypoxia. The by far most commonly used molecular imaging technique in oncology is, however, positron emission tomography (PET) with the glucose analog [ 18 F]fluorodeoxyglucose (FDG-PET). FDG-PET permits non-invasive quantitative assessment of the accelerated exogenous glucose use of malignant tumors. Numerous studies have now shown that reduction of tumor FDG-uptake during therapy allows early prediction of tumor response and patient survival. Clinical studies are currently underway to determine whether FDG-PET can be used to individualize tumor therapy by signaling early in the course of therapy the need for therapeutic adjustments in patients with likely non-responding tumors. (orig.)

  9. Dynamic molecular imaging of cardiac innervation using a dual head pinhole SPECT system

    International Nuclear Information System (INIS)

    Hu, Jicun; Boutchko, Rostyslav; Sitek, Arkadiusz; Reutter, BryanW.; Huesman, Ronald H.; Gullberg, Grant T.

    2008-01-01

    Typically 123I-MIBG is used for the study of innervation and function of the sympathetic nervous system in heart failure. The protocol involves two studies: first a planar or SPECT scan is performed to measure initial uptake of the tracer, followed some 3-4 hours later by another study measuring the wash-out of the tracer from the heart. A fast wash-out is indicative of a compromised heart. In this work, a dual head pinhole SPECT system was used for imaging the distribution and kinetics of 123I-MIBG in the myocardium of spontaneous hypertensive rats (SHR) and normotensive Wistar Kyoto (WKY) rats. The system geometry was calibrated based on a nonlinear point projection fitting method using a three-point source phantom. The angle variation effect of the parameters was modeled with a sinusoidal function. A dynamic acquisition was performed by injecting 123I-MIBG into rats immediately after starting the data acquisition. The detectors rotated continuously performing a 360o data acquisition every 90 seconds. We applied the factor analysis (FA)method and region of interest (ROI) sampling method to obtain time activity curves (TACs)in the blood pool and myocardium and then applied two-compartment modeling to estimate the kinetic parameters. Since the initial injection bolus is too fast for obtaining a consistent tomographic data set in the first few minutes of the study, we applied the FA method directly to projections during the first rotation. Then the time active curves for blood and myocardial tissue were obtained from ROI sampling. The method was applied to determine if there were differences in the kinetics between SHR and WKY rats and requires less time by replacing the delayed scan at 3-4 hours after injection with a dynamic acquisition over 90 to 120 minutes. The results of a faster washout and a smaller distribution volume of 123I-MIBG near the end of life in the SHR model of hypertrophic cardiomyopthy may be indicative of a failing heart in late stages of heart

  10. Dynamic molecular imaging of cardiac innervation using a dual headpinhole SPECT system

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jicun; Boutchko, Rostyslav; Sitek, Arkadiusz; Reutter, BryanW.; Huesman, Ronald H.; Gullberg, Grant T.

    2008-03-29

    Typically 123I-MIBG is used for the study of innervation andfunction of the sympathetic nervous system in heart failure. The protocolinvolves two studies: first a planar or SPECT scan is performed tomeasure initial uptake of the tracer, followed some 3-4 hours later byanother study measuring the wash-out of the tracer from the heart. A fastwash-out is indicative of a compromised heart. In this work, a dual headpinhole SPECT system was used for imaging the distribution and kineticsof 123I-MIBG in the myocardium of spontaneous hypertensive rats (SHR) andnormotensive Wistar Kyoto (WKY) rats. The system geometry was calibratedbased on a nonlinear point projection fitting method using a three-pointsource phantom. The angle variation effect of the parameters was modeledwith a sinusoidal function. A dynamic acquisition was performed byinjecting 123I-MIBG into rats immediately after starting the dataacquisition. The detectors rotated continuously performing a 360o dataacquisition every 90 seconds. We applied the factor analysis (FA)methodand region of interest (ROI) sampling method to obtain time activitycurves (TACs)in the blood pool and myocardium and then appliedtwo-compartment modeling to estimate the kinetic parameters. Since theinitial injection bolus is too fast for obtaining a consistenttomographic data set in the first few minutes of the study, we appliedthe FA method directly to projections during the first rotation. Then thetime active curves for blood and myocardial tissue were obtained from ROIsampling. The method was applied to determine if there were differencesin the kinetics between SHR and WKY rats and requires less time byreplacing the delayed scan at 3-4 hours after injection with a dynamicacquisition over 90 to 120 minutes. The results of a faster washout and asmaller distribution volume of 123IMIBG near the end of life in the SHRmodel of hypertrophic cardiomyopthy may be indicative of a failing heartin late stages of heart failure.

  11. Molecular MR imaging

    International Nuclear Information System (INIS)

    Fleige, G.; Hamm, B.

    2000-01-01

    Basic medicobiological research in recent years has made rapid advances in the functional understanding of normal and pathological processes down to the molecular level. At the same time, various imaging modalities have developed from the depiction of organs to approaching the depiction of the cellular level and are about to make the visualization of molecular processes an established procedure. Besides other modalities like PET and near-infrared fluorescence, MR imaging offers some promising options for molecular imaging as well as some applications that have already been tested such as the visualization of enzyme activity, the depiction of the expression of certain genes, the visualization of surface receptors, or the specific demonstration of cells involved in the body's immune response. A major advantage of molecular magnetic resonance imaging (mMRI) over other more sensitive modalities is its high spatial resolution. However, the establishment of mMRI crucially relies on further improvements in resolution and the development of molecular markers for improving its sensitivity and specificity. The state of the art of mMRI is presented by giving a survey of the literature on experimental studies and reporting the results our study group obtained during investigation on gliomas. (orig.) [de

  12. 3D molecular imaging SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Gillen, Greg [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States)]. E-mail: Greg.gillen@nist.gov; Fahey, Albert [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States); Wagner, Matt [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States); Mahoney, Christine [Surface and Microanalysis Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8371 (United States)

    2006-07-30

    Thin monolayer and bilayer films of spin cast poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), poly(lactic) acid (PLA) and PLA doped with several pharmaceuticals have been analyzed by dynamic SIMS using SF{sub 5} {sup +} polyatomic primary ion bombardment. Each of these systems exhibited minimal primary beam-induced degradation under cluster ion bombardment allowing molecular depth profiles to be obtained through the film. By combing secondary ion imaging with depth profiling, three-dimensional molecular image depth profiles have been obtained from these systems. In another approach, bevel cross-sections are cut in the samples with the SF{sub 5} {sup +} primary ion beam to produce a laterally magnified cross-section of the sample that does not contain the beam-induced damage that would be induced by conventional focussed ion beam (FIB) cross-sectioning. The bevel surface can then be examined using cluster SIMS imaging or other appropriate microanalysis technique.

  13. Molecular imaging II

    International Nuclear Information System (INIS)

    Semmler, Wolfhard; Schwaiger, Markus

    2008-01-01

    The aim of this textbook of molecular imaging is to provide an up to date review of this rapidly growing field and to discuss basic methodological aspects necessary for the interpretation of experimental and clinical results. Emphasis is placed on the interplay of imaging technology and probe development, since the physical properties of the imaging approach need to be closely linked with the biologic application of the probe (i.e. nanoparticles and microbubbles). Various chemical strategies are discussed and related to the biologic applications. Reporter-gene imaging is being addressed not only in experimental protocols, but also first clinical applications are discussed. Finally, strategies of imaging to characterize apoptosis and angiogenesis are described and discussed in the context of possible clinical translation. (orig.)

  14. Computational methods for molecular imaging

    CERN Document Server

    Shi, Kuangyu; Li, Shuo

    2015-01-01

    This volume contains original submissions on the development and application of molecular imaging computing. The editors invited authors to submit high-quality contributions on a wide range of topics including, but not limited to: • Image Synthesis & Reconstruction of Emission Tomography (PET, SPECT) and other Molecular Imaging Modalities • Molecular Imaging Enhancement • Data Analysis of Clinical & Pre-clinical Molecular Imaging • Multi-Modal Image Processing (PET/CT, PET/MR, SPECT/CT, etc.) • Machine Learning and Data Mining in Molecular Imaging. Molecular imaging is an evolving clinical and research discipline enabling the visualization, characterization and quantification of biological processes taking place at the cellular and subcellular levels within intact living subjects. Computational methods play an important role in the development of molecular imaging, from image synthesis to data analysis and from clinical diagnosis to therapy individualization. This work will bring readers fro...

  15. The nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-03-01

    MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

  16. Imaging the reactions of molecular dications: a new probe of dicationic reaction dynamics and energetics

    International Nuclear Information System (INIS)

    Wan-Ping Hu, S.; Harper, S.M.; Price, S.D.

    2002-01-01

    Experiments which generated angularly resolved data to prove the dynamics of dication chemical reactions were performed using a position sensitive coincidence (PSCO) apparatus, to detect in coincidence both of the charged products from such reaction. It consists of a ion source, a hemispherical energy analyser, and a time-of-flight mass spectrometer. Initial experiments to test the apparatus performance were runned on the atomic electron transfer reaction: Ne 2+ + Ar → Ne + + Ar + . Angular distributions, translational and internal energies of the product ions were extracted, as well as the scattering diagram among other data. (nevyjel)

  17. Molecular imaging in biomedical research

    International Nuclear Information System (INIS)

    Jagannathan, N.R.

    2007-01-01

    Molecular imaging (MI) is a diverse technology that revolutionized preclinical, clinical and drug-discovery research. It integrates biology and medicine, and the technique presents a unique opportunity to examine living systems in vivo as a dynamic biological system. It is a hybrid technology that combines PET, SPECT, ultrasound, optical imaging and MR. Several MI methodologies are developed to examine the integrative functions of molecules, cells, organ systems and whole organisms. MI is superior to conventional diagnostic techniques in allowing better staging as well as to monitor the response of cancer/tumour to treatment. In addition, it helps visualization of specific molecular targets or pathways and cells in living systems and ultimately in the clinic. (author)

  18. Molecular imaging of transcriptional regulation during inflammation

    Directory of Open Access Journals (Sweden)

    Carlsen Harald

    2010-04-01

    Full Text Available Abstract Molecular imaging enables non-invasive visualization of the dynamics of molecular processes within living organisms in vivo. Different imaging modalities as MRI, SPECT, PET and optic imaging are used together with molecular probes specific for the biological process of interest. Molecular imaging of transcription factor activity is done in animal models and mostly in transgenic reporter mice, where the transgene essentially consists of a promoter that regulates a reporter gene. During inflammation, the transcription factor NF-κB is widely involved in orchestration and regulation of the immune system and almost all imaging studies in this field has revolved around the role and regulation of NF-κB. We here present a brief introduction to experimental use and design of transgenic reporter mice and a more extensive review of the various studies where molecular imaging of transcriptional regulation has been applied during inflammation.

  19. Molecular Biomedical Imaging Laboratory (MBIL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Molecular Biomedical Imaging Laboratory (MBIL) is adjacent-a nd has access-to the Department of Radiology and Imaging Sciences clinical imaging facilities. MBIL...

  20. Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

  1. Nuclear medicine imaging instrumentations for molecular imaging

    International Nuclear Information System (INIS)

    Chung, Yong Hyun; Song, Tae Yong; Choi, Yong

    2004-01-01

    Small animal models are extensively utilized in the study of biomedical sciences. Current animal experiments and analysis are largely restricted to in vitro measurements and need to sacrifice animals to perform tissue or molecular analysis. This prevents researchers from observing in vivo the natural evolution of the process under study. Imaging techniques can provide repeatedly in vivo anatomic and molecular information noninvasively. Small animal imaging systems have been developed to assess biological process in experimental animals and increasingly employed in the field of molecular imaging studies. This review outlines the current developments in nuclear medicine imaging instrumentations including fused multi-modality imaging systems for small animal imaging

  2. Molecular nuclear cardiac imaging

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong Soo; Paeng, Jin Chul [College of Medicine, Seoul National Univ., Seoul (Korea, Republic of)

    2004-04-01

    Molecular nuclear cardiac imaging has included Tc-99m Annexin imaging to visualize myocardial apoptosis, but is now usually associated with gene therapy and cell-based therapy. Cardiac gene therapy was not successful so far but cardiac reporter gene imaging was made possible using HSV-TK (herpes simplex virus thymidine kinase) and F-18 FHBG (fluoro-hydroxymethylbutyl guanine) or I-124 FIAU (fluoro-deoxyiodo-arabino-furanosyluracil). Gene delivery was performed by needle injection with or without catheter guidance. TK expression did not last longer than 2 weeks in myocardium. Cell-based therapy of ischemic heart or failing heart looks promising, but biodistribution and differentiation of transplanted cells are not known. Reporter genes can be transfected to the stem/progenitor cells and cells containing these genes can be transplanted to the recipients using catheter-based purging or injection. Repeated imaging should be available and if promoter are varied to let express reporter transgenes, cellular (trans)differentiation can be studied. NIS (sodium iodide symporter) or D2R receptor genes are promising in this aspect.

  3. Molecular nuclear cardiac imaging

    International Nuclear Information System (INIS)

    Lee, Dong Soo; Paeng, Jin Chul

    2004-01-01

    Molecular nuclear cardiac imaging has included Tc-99m Annexin imaging to visualize myocardial apoptosis, but is now usually associated with gene therapy and cell-based therapy. Cardiac gene therapy was not successful so far but cardiac reporter gene imaging was made possible using HSV-TK (herpes simplex virus thymidine kinase) and F-18 FHBG (fluoro-hydroxymethylbutyl guanine) or I-124 FIAU (fluoro-deoxyiodo-arabino-furanosyluracil). Gene delivery was performed by needle injection with or without catheter guidance. TK expression did not last longer than 2 weeks in myocardium. Cell-based therapy of ischemic heart or failing heart looks promising, but biodistribution and differentiation of transplanted cells are not known. Reporter genes can be transfected to the stem/progenitor cells and cells containing these genes can be transplanted to the recipients using catheter-based purging or injection. Repeated imaging should be available and if promoter are varied to let express reporter transgenes, cellular (trans)differentiation can be studied. NIS (sodium iodide symporter) or D2R receptor genes are promising in this aspect

  4. IMAGING MOLECULAR FRAME DYNAMICS

    DEFF Research Database (Denmark)

    Hansen, Jonas Lerche

    2012-01-01

    Molekylererikkeblotfastestrukturersomnårdetegnespåetstykkepapir. Tværtimod er de altid i bevægelse, hvilket betyder at selv stive molekyler på gasform vil kunne rotere frit i forhold til hinanden. En sådan samling af molekyler betegnes som tilfældigt orienterede. I mange eksperimenter er denne ti...

  5. Molecular dynamics of bacteriorhodopsin.

    Science.gov (United States)

    Lupo, J A; Pachter, R

    1997-02-01

    A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.

  6. Quantitative analysis of CTEM images of small dislocation loops in Al and stacking fault tetrahedra in Cu generated by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Schaeublin, R.; Almazouzi, A.; Dai, Y.; Osetsky, Yu.N.; Victoria, M.

    2000-01-01

    The visibility of conventional transmission electron microscopy (CTEM) images of small crystalline defects generated by molecular dynamics (MD) simulation is investigated. Faulted interstitial dislocation loops in Al smaller than 2 nm in diameter and stacking fault tetrahedra (SFT) in Cu smaller than 4 nm in side are assessed. A recent approach allowing to simulate the CTEM images of computer generated samples described by their atomic positions is applied to obtain bright field and weak beam images. For the dislocation loop-like cluster it appears that the simulated image is comparable to experimental images. The contrast of the g(3.1g) near weak beam image decreases with decreasing size of the cluster but is still 20% of the background intensity for a 2 interstitial cluster. This indicates a visibility at the limit of the experimental background noise. In addition, the cluster image size, which is here always larger than the real size, saturates at about 1 nm when the cluster real size decreases below 1 nm, which corresponds to a cluster of 8 interstitials. For the SFT in Cu the g(6.1g) weak beam image is comparable to experimental images. It appears that the image size is larger than the real size by 20%. A large loss of the contrast features that allows to identify an SFT is observed on the image of the smallest SFT (21 vacancies)

  7. Molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Dehmer, J.L.

    1982-01-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed

  8. Physical adsorption and molecular dynamics

    International Nuclear Information System (INIS)

    Cohan, N.V.

    1981-01-01

    Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

  9. Dynamic Optically Multiplexed Imaging

    Science.gov (United States)

    2015-07-29

    Dynamic Optically Multiplexed Imaging Yaron Rachlin, Vinay Shah, R. Hamilton Shepard, and Tina Shih Lincoln Laboratory, Massachusetts Institute of...V. Shah, and T. Shih “Design Architectures for Optically Multiplexed Imaging,” in submission 9 R. Gupta , P. Indyk, E. Price, and Y. Rachlin

  10. Cardiovascular molecular imaging of apoptosis

    International Nuclear Information System (INIS)

    Wolters, S.L.; Reutelingsperger, C.P.M.; Corsten, M.F.; Hofstra, L.; Narula, J.

    2007-01-01

    Molecular imaging strives to visualise processes at the molecular and cellular level in vivo. Understanding these processes supports diagnosis and evaluation of therapeutic efficacy on an individual basis and thereby makes personalised medicine possible. Apoptosis is a well-organised mode of cell suicide that plays a role in cardiovascular diseases (CVD). Apoptosis is associated with loss of cardiomyocytes following myocardial infarction, atherosclerotic plaque instability, congestive heart failure and allograft rejection of the transplanted heart. Thus, apoptosis constitutes an attractive target for molecular imaging of CVD. Our current knowledge about the molecular players and mechanisms underlying apoptosis offers a rich palette of potential molecular targets for molecular imaging. However, only a few have been successfully developed so far. This review highlights aspects of the molecular machinery and biochemistry of apoptosis relevant to the development of molecular imaging probes. It surveys the role of apoptosis in four major areas of CVD and portrays the importance and future perspectives of apoptosis imaging. The annexin A5 imaging protocol is emphasised since it is the most advanced protocol to measure apoptosis in both preclinical and clinical studies. (orig.)

  11. Cardiovascular molecular imaging of apoptosis

    Energy Technology Data Exchange (ETDEWEB)

    Wolters, S.L.; Reutelingsperger, C.P.M. [Maastricht University, Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht (Netherlands); Corsten, M.F.; Hofstra, L. [Maastricht University, Department of Cardiology, Cardiovascular Research Institute Maastricht, P.O. Box 616, Maastricht (Netherlands); Narula, J. [University of California Irvine, Department of Cardiology, Irvine (United States)

    2007-06-15

    Molecular imaging strives to visualise processes at the molecular and cellular level in vivo. Understanding these processes supports diagnosis and evaluation of therapeutic efficacy on an individual basis and thereby makes personalised medicine possible. Apoptosis is a well-organised mode of cell suicide that plays a role in cardiovascular diseases (CVD). Apoptosis is associated with loss of cardiomyocytes following myocardial infarction, atherosclerotic plaque instability, congestive heart failure and allograft rejection of the transplanted heart. Thus, apoptosis constitutes an attractive target for molecular imaging of CVD. Our current knowledge about the molecular players and mechanisms underlying apoptosis offers a rich palette of potential molecular targets for molecular imaging. However, only a few have been successfully developed so far. This review highlights aspects of the molecular machinery and biochemistry of apoptosis relevant to the development of molecular imaging probes. It surveys the role of apoptosis in four major areas of CVD and portrays the importance and future perspectives of apoptosis imaging. The annexin A5 imaging protocol is emphasised since it is the most advanced protocol to measure apoptosis in both preclinical and clinical studies. (orig.)

  12. Molecular photoacoustic imaging

    Directory of Open Access Journals (Sweden)

    Frogh Jafarian Dehkordi

    2015-04-01

    Full Text Available Background: Hybrid imaging modalities which simultaneously benefit from capabilities of combined modalities provides an opportunity to modify quality of the images which can be obtained by each of the combined imaging systems. One of the imaging modalities, emerged in medical research area as a hybrid of ultrasound imaging and optical imaging, is photoacoustic imaging which apply ultrasound wave generated by tissue, after receiving laser pulse, to produce medical images. Materials and Methods: In this review, using keywords such as photoacoustic, optoacoustic, laser-ultrasound, thermoacoustic at databases such as PubMed and ISI, studies performed in the field of photoacoustic and related findings were evaluated. Results: Photoacoustic imaging, acquiring images with high contrast and desired resolution, provides an opportunity to perform physiologic and anatomic studies. Because this technique does not use ionizing radiation, it is not restricted by the limitation of the ionizing-based imaging systems therefore it can be used noninvasively to make images from cell, vessels, whole body imaging of the animal and distinguish tumor from normal tissue. Conclusion: Photoacoustic imaging is a new method in preclinical researches which can be used in various physiologic and anatomic studies. This method, because of application of non-ionizing radiation, may resolve limitation of radiation based method in diagnostic assessments.

  13. Molecular Imaging of Inflammation in Atherosclerosis

    Science.gov (United States)

    Wildgruber, Moritz; Swirski, Filip K.; Zernecke, Alma

    2013-01-01

    Acute rupture of vulnerable plaques frequently leads to myocardial infarction and stroke. Within the last decades, several cellular and molecular players have been identified that promote atherosclerotic lesion formation, maturation and plaque rupture. It is now widely recognized that inflammation of the vessel wall and distinct leukocyte subsets are involved throughout all phases of atherosclerotic lesion development. The mechanisms that render a stable plaque unstable and prone to rupture, however, remain unknown and the identification of the vulnerable plaque remains a major challenge in cardiovascular medicine. Imaging technologies used in the clinic offer minimal information about the underlying biology and potential risk for rupture. New imaging technologies are therefore being developed, and in the preclinical setting have enabled new and dynamic insights into the vessel wall for a better understanding of this complex disease. Molecular imaging has the potential to track biological processes, such as the activity of cellular and molecular biomarkers in vivo and over time. Similarly, novel imaging technologies specifically detect effects of therapies that aim to stabilize vulnerable plaques and silence vascular inflammation. Here we will review the potential of established and new molecular imaging technologies in the setting of atherosclerosis, and discuss the cumbersome steps required for translating molecular imaging approaches into the clinic. PMID:24312156

  14. Gas Phase Molecular Dynamics

    International Nuclear Information System (INIS)

    Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

    1999-01-01

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wave packet calculations that provide insights into energy flow between the vibrational modes of the molecule

  15. Molecular imaging in cardiovascular diseases

    International Nuclear Information System (INIS)

    Botnar, R.M.; Ebersberger, H.; Noerenberg, D.

    2015-01-01

    Cardiovascular diseases remain the leading cause of morbidity and mortality in industrialized and developing countries. In clinical practice, the in-vivo identification of atherosclerotic lesions, which can lead to complications such as heart attack or stroke, remains difficult. Imaging techniques provide the reference standard for the detection of clinically significant atherosclerotic changes in the coronary and carotid arteries. The assessment of the luminal narrowing is feasible, while the differentiation of stable and potentially unstable or vulnerable atherosclerotic plaques is currently not possible using non-invasive imaging. With high spatial resolution and high soft tissue contrast, magnetic resonance imaging (MRI) is a suitable method for the evaluation of the thin arterial wall. In clinical practice, native MRI of the vessel wall already allows the differentiation and characterization of components of atherosclerotic plaques in the carotid arteries and the aorta. Additional diagnostic information can be gained by the use of non-specific MRI contrast agents. With the development of targeted molecular probes, that highlight specific molecules or cells, pathological processes can be visualized at a molecular level with high spatial resolution. In this review article, the development of pathophysiological changes leading to the development of the arterial wall are introduced and discussed. Additionally, principles of contrast enhanced imaging with non-specific contrast agents and molecular probes will be discussed and latest developments in the field of molecular imaging of the vascular wall will be introduced.

  16. Molecular imaging. Fundamentals and applications

    International Nuclear Information System (INIS)

    Tian, Jie

    2013-01-01

    Covers a wide range of new theory, new techniques and new applications. Contributed by many experts in China. The editor has obtained the National Science and Technology Progress Award twice. ''Molecular Imaging: Fundamentals and Applications'' is a comprehensive monograph which describes not only the theory of the underlying algorithms and key technologies but also introduces a prototype system and its applications, bringing together theory, technology and applications. By explaining the basic concepts and principles of molecular imaging, imaging techniques, as well as research and applications in detail, the book provides both detailed theoretical background information and technical methods for researchers working in medical imaging and the life sciences. Clinical doctors and graduate students will also benefit from this book.

  17. Thomas-Fermi molecular dynamics

    International Nuclear Information System (INIS)

    Clerouin, J.; Pollock, E.L.; Zerah, G.

    1992-01-01

    A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

  18. Symmetry of quantum molecular dynamics

    International Nuclear Information System (INIS)

    Burenin, A.V.

    2002-01-01

    The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

  19. General perspectives for molecular nuclear imaging

    International Nuclear Information System (INIS)

    Chung, June Key

    2004-01-01

    Molecular imaging provides a visualization of normal as well as abnormal cellular processes at a molecular or genetic level rather than at an anatomical level. Conventional medical imaging methods utilize the imaging signals produced by nonspecific physico-chemical interaction. However, molecular imaging methods utilize the imaging signals derived from specific cellular or molecular events. Because molecular and genetic changes precede anatomical change in the course of disease development, molecular imaging can detect early events in disease progression. In the near future, through molecular imaging we can understand basic mechanisms of disease, and diagnose earlier and, subsequently, treat earlier intractable disease such as cancer, neuro-degenerative diseases, and immunologic disorders. In beginning period, nuclear medicine started as a molecular imaging, and has had a leading role in the field of molecular imaging. But recently molecular imaging has been rapidly developed. Besides nuclear imaging, molecular imaging methods such as optical imaging, magnetic resonance imaging are emerging. Each imaging modalities have their advantages and weaknesses. The opportunities from molecular imaging look bright. We should try nuclear medicine continues to have a leading role in molecular imaging

  20. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

    Directory of Open Access Journals (Sweden)

    Fabiana A Caetano

    2015-12-01

    Full Text Available Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

  1. Quantum dynamic imaging theoretical and numerical methods

    CERN Document Server

    Ivanov, Misha

    2011-01-01

    Studying and using light or "photons" to image and then to control and transmit molecular information is among the most challenging and significant research fields to emerge in recent years. One of the fastest growing areas involves research in the temporal imaging of quantum phenomena, ranging from molecular dynamics in the femto (10-15s) time regime for atomic motion to the atto (10-18s) time scale of electron motion. In fact, the attosecond "revolution" is now recognized as one of the most important recent breakthroughs and innovations in the science of the 21st century. A major participant in the development of ultrafast femto and attosecond temporal imaging of molecular quantum phenomena has been theory and numerical simulation of the nonlinear, non-perturbative response of atoms and molecules to ultrashort laser pulses. Therefore, imaging quantum dynamics is a new frontier of science requiring advanced mathematical approaches for analyzing and solving spatial and temporal multidimensional partial differ...

  2. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  3. Quantitative Methods for Molecular Diagnostic and Therapeutic Imaging

    OpenAIRE

    Li, Quanzheng

    2013-01-01

    This theme issue provides an overview on the basic quantitative methods, an in-depth discussion on the cutting-edge quantitative analysis approaches as well as their applications for both static and dynamic molecular diagnostic and therapeutic imaging.

  4. Molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

  5. Molecular dynamics for dense matter

    Science.gov (United States)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

  6. Molecular imaging by cardiovascular MR.

    Science.gov (United States)

    Cyrus, Tillmann; Lanza, Gregory M; Wickline, Samuel A

    2007-01-01

    Do molecularly-targeted contrast agents have what it takes to usher in a paradigm shift as to how we will image cardiovascular disease in the near future? Moreover, are non-invasive vulnerable plaque detection and preemptive treatments with these novel nanoparticulate agents within reach for clinical applications? In this article, we attempt to make a compelling case for how the advent of molecularly-targeted nanoparticle technology may change the way we detect atherosclerotic lesions, determine their clinical significance and even provide non-invasive treatments. Focusing on imaging with cardiovascular MR, an overview of the latest developments in this rapidly evolving field of so-called "intelligent" contrast agents that are able to interrogate the vascular wall and various complementary advanced imaging technologies are presented.

  7. Molecular imaging in cervical cancer

    International Nuclear Information System (INIS)

    KHAN, Sairah R.; ROCKALL, Andrea G.; BARWICK, Tara D.

    2016-01-01

    Despite the development of screening and of a vaccine, cervix cancer is a major cause of cancer death in young women worldwide. A third of women treated for the disease will recur, almost inevitably leading to death. Functional imaging has the potential to stratify patients at higher risk of poor response or relapse by improved delineation of disease extent and tumor characteristics. A number of molecular imaging biomarkers have been shown to predict outcome at baseline and/or early during therapy in cervical cancer. In future this could help tailor the treatment plan which could include selection of patients for close follow up, adjuvant therapy or trial entry for novel agents or adaptive clinical trials. The use of molecular imaging techniques, FDG PET/CT and functional MRI, in staging and response assessment of cervical cancer is reviewed.

  8. Molecular Imaging Challenges With PET

    CERN Document Server

    Lecoq, P

    2010-01-01

    The future trends in molecular imaging and associated challenges for in-vivo functional imaging are illustrated on the basis of a few examples, such as atherosclerosis vulnerable plaques imaging or stem cells tracking. A set of parameters are derived to define the specifications of a new generation of in-vivo imaging devices in terms of sensitivity, spatial resolution and signal-to-noise ratio. The limitations of strategies used in present PET scanners are discussed and new approaches are proposed taking advantage of recent progress on materials, photodetectors and readout electronics. A special focus is put on metamaterials, as a new approach to bring more functionality to detection devices. It is shown that the route is now open towards a fully digital detector head with very high photon counting capability over a large energy range, excellent timing precision and possibility of imaging the energy deposition process.

  9. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  10. Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

    International Nuclear Information System (INIS)

    Perez, Danny

    2012-01-01

    We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

  11. Cancer Stratification by Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Justus Weber

    2015-03-01

    Full Text Available The lack of specificity of traditional cytotoxic drugs has triggered the development of anticancer agents that selectively address specific molecular targets. An intrinsic property of these specialized drugs is their limited applicability for specific patient subgroups. Consequently, the generation of information about tumor characteristics is the key to exploit the potential of these drugs. Currently, cancer stratification relies on three approaches: Gene expression analysis and cancer proteomics, immunohistochemistry and molecular imaging. In order to enable the precise localization of functionally expressed targets, molecular imaging combines highly selective biomarkers and intense signal sources. Thus, cancer stratification and localization are performed simultaneously. Many cancer types are characterized by altered receptor expression, such as somatostatin receptors, folate receptors or Her2 (human epidermal growth factor receptor 2. Similar correlations are also known for a multitude of transporters, such as glucose transporters, amino acid transporters or hNIS (human sodium iodide symporter, as well as cell specific proteins, such as the prostate specific membrane antigen, integrins, and CD20. This review provides a comprehensive description of the methods, targets and agents used in molecular imaging, to outline their application for cancer stratification. Emphasis is placed on radiotracers which are used to identify altered expression patterns of cancer associated markers.

  12. Rheology via nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1982-10-01

    The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

  13. Molecular imaging in neurology and neuroscience

    International Nuclear Information System (INIS)

    Schreckenberger, M.

    2007-01-01

    Molecular imaging in neurology and neuroscience is a suspenseful and fast developing tool in order to quantitatively image genomics and proteomics by means of direct and indirect markers. Because of its high-sensitive tracer principle, nuclear medicine imaging has the pioneering task for the methodical progression of molecular imaging. The current development of molecular imaging in neurology changes from the use of indirect markers of gene and protein expression to the direct imaging of the molecular mechanisms. It is the aim of this article to give a short review on the status quo of molecular imaging in neurology with emphasis on clinically relevant aspects. (orig.)

  14. Laser Controlled Molecular Orientation Dynamics

    International Nuclear Information System (INIS)

    Atabek, O.

    2004-01-01

    Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

  15. Molecular dynamics study of silver

    International Nuclear Information System (INIS)

    Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

    1995-03-01

    We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

  16. Final Report Product Imaging of Molecular Dynamics Relevant to Combustion Grant No. DE-FG02-88ER13934

    International Nuclear Information System (INIS)

    Houston, Paul L.

    2005-01-01

    Product imaging has been used to investigate several processes important to a fundamental understanding of combustion. The imaging technique produces a ''snapshot'' of the three-dimensional velocity distribution of a state-selected reaction product. Research in three main areas is planned or underway. First, product imaging has been used to investigate the reactive scattering of radicals or atoms with species important in combustion. These experiments, while more difficult than studies of inelastic scattering or photodissociation, are now becoming feasible. They provide both product distributions of important processes as well as angular information important to the interpretation of reaction mechanisms. Second, the imaging technique has been used to measure rotationally inelastic energy transfer on collision of closed-shell species with important combustion radicals. Such measurements improve our knowledge of intramolecular potentials and provide important tests of ab initio calculations. Finally, experiments using product imaging have explored the vacuum ultraviolet photodissociation of O2, N2O, SO2, CO2 and other important species. Little is known about the highly excited electronic states of these molecules and, in particular, how they dissociate. These studies provide product vibrational energy distributions as well as angular information that can aid in understanding the symmetry and crossings among the excited electronic states

  17. Imaging molecular interactions in cells by dynamic and static fluorescence anisotropy (rFLIM and emFRET)

    NARCIS (Netherlands)

    Lidke, D.S.; Nagy, P.; Barisas, B.G.; Heintzmann, R.; Post, Janine Nicole; Lidke, K.A.; Clayton, A.H.A.; Arndt-jovin, D.J.; Jovin, T.M.

    2003-01-01

    We report the implementation and exploitation of fluorescence polarization measurements, in the form of anisotropy fluorescence lifetime imaging microscopy (rFLIM) and energy migration Förster resonance energy transfer (emFRET) modalities, for wide-field, confocal laser-scanning microscopy and flow

  18. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

  19. A concurrent multiscale micromorphic molecular dynamics

    International Nuclear Information System (INIS)

    Li, Shaofan; Tong, Qi

    2015-01-01

    In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

  20. Color molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Hatsuda, Tetsuo

    2000-01-01

    We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

  1. Molecular dynamics of liquid crystals

    Science.gov (United States)

    Sarman, Sten

    1997-02-01

    We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.

  2. Introduction to basic molecular biologic techniques for molecular imaging researches

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2004-01-01

    Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

  3. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

    This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

  4. Molecular imaging: current status and emerging strategies

    International Nuclear Information System (INIS)

    Pysz, M.A.; Gambhir, S.S.; Willmann, J.K.

    2010-01-01

    In vivo molecular imaging has a great potential to impact medicine by detecting diseases in early stages (screening), identifying extent of disease, selecting disease- and patient-specific treatment (personalized medicine), applying a directed or targeted therapy, and measuring molecular-specific effects of treatment. Current clinical molecular imaging approaches primarily use positron-emission tomography (PET) or single photon-emission computed tomography (SPECT)-based techniques. In ongoing preclinical research, novel molecular targets of different diseases are identified and, sophisticated and multifunctional contrast agents for imaging these molecular targets are developed along with new technologies and instrumentation for multi-modality molecular imaging. Contrast-enhanced molecular ultrasound (US) with molecularly-targeted contrast microbubbles is explored as a clinically translatable molecular imaging strategy for screening, diagnosing, and monitoring diseases at the molecular level. Optical imaging with fluorescent molecular probes and US imaging with molecularly-targeted microbubbles are attractive strategies as they provide real-time imaging, are relatively inexpensive, produce images with high spatial resolution, and do not involve exposure to ionizing irradiation. Raman spectroscopy/microscopy has emerged as a molecular optical imaging strategy for ultrasensitive detection of multiple biomolecules/biochemicals with both in vivo and ex vivo versatility. Photoacoustic imaging is a hybrid of optical and US techniques involving optically-excitable molecularly-targeted contrast agents and quantitative detection of resulting oscillatory contrast agent movement with US. Current preclinical findings and advances in instrumentation, such as endoscopes and microcatheters, suggest that these molecular imaging methods have numerous potential clinical applications and will be translated into clinical use in the near future.

  5. Molecular-resolution imaging of pentacene on KCl(001

    Directory of Open Access Journals (Sweden)

    Julia L. Neff

    2012-02-01

    Full Text Available The growth of pentacene on KCl(001 at submonolayer coverage was studied by dynamic scanning force microscopy. At coverages below one monolayer pentacene was found to arrange in islands with an upright configuration. The molecular arrangement was resolved in high-resolution images. In these images two different types of patterns were observed, which switch repeatedly. In addition, defects were found, such as a molecular vacancy and domain boundaries.

  6. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

  7. Nanomedicine: Perspective and promises with ligand-directed molecular imaging

    Energy Technology Data Exchange (ETDEWEB)

    Pan Dipanjan [Department of Medicine, Washington University Medical School, St. Louis, MO (United States)], E-mail: dipanjan@wustl.edu; Lanza, Gregory M.; Wickline, Samuel A. [Department of Medicine, Washington University Medical School, St. Louis, MO (United States); Caruthers, Shelton D. [Department of Medicine, Washington University Medical School, St. Louis, MO (United States); Philips Healthcare, Andover, MA (United States)], E-mail: scaruthers@cmrl.wustl.edu

    2009-05-15

    Molecular imaging and targeted drug delivery play an important role toward personalized medicine, which is the future of patient management. Of late, nanoparticle-based molecular imaging has emerged as an interdisciplinary area, which shows promises to understand the components, processes, dynamics and therapies of a disease at a molecular level. The unprecedented potential of nanoplatforms for early detection, diagnosis and personalized treatment of diseases, have found application in every biomedical imaging modality. Biological and biophysical barriers are overcome by the integration of targeting ligands, imaging agents and therapeutics into the nanoplatform which allow for theranostic applications. In this article, we have discussed the opportunities and potential of targeted molecular imaging with various modalities putting a particular emphasis on perfluorocarbon nanoemulsion-based platform technology.

  8. Nanomedicine: Perspective and promises with ligand-directed molecular imaging

    International Nuclear Information System (INIS)

    Pan Dipanjan; Lanza, Gregory M.; Wickline, Samuel A.; Caruthers, Shelton D.

    2009-01-01

    Molecular imaging and targeted drug delivery play an important role toward personalized medicine, which is the future of patient management. Of late, nanoparticle-based molecular imaging has emerged as an interdisciplinary area, which shows promises to understand the components, processes, dynamics and therapies of a disease at a molecular level. The unprecedented potential of nanoplatforms for early detection, diagnosis and personalized treatment of diseases, have found application in every biomedical imaging modality. Biological and biophysical barriers are overcome by the integration of targeting ligands, imaging agents and therapeutics into the nanoplatform which allow for theranostic applications. In this article, we have discussed the opportunities and potential of targeted molecular imaging with various modalities putting a particular emphasis on perfluorocarbon nanoemulsion-based platform technology.

  9. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

    2009-01-01

    We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

  10. Molecular imaging promotes progress in orthopedic research.

    Science.gov (United States)

    Mayer-Kuckuk, Philipp; Boskey, Adele L

    2006-11-01

    Modern orthopedic research is directed towards the understanding of molecular mechanisms that determine development, maintenance and health of musculoskeletal tissues. In recent years, many genetic and proteomic discoveries have been made which necessitate investigation under physiological conditions in intact, living tissues. Molecular imaging can meet this demand and is, in fact, the only strategy currently available for noninvasive, quantitative, real-time biology studies in living subjects. In this review, techniques of molecular imaging are summarized, and applications to bone and joint biology are presented. The imaging modality most frequently used in the past was optical imaging, particularly bioluminescence and near-infrared fluorescence imaging. Alternate technologies including nuclear and magnetic resonance imaging were also employed. Orthopedic researchers have applied molecular imaging to murine models including transgenic mice to monitor gene expression, protein degradation, cell migration and cell death. Within the bone compartment, osteoblasts and their stem cells have been investigated, and the organic and mineral bone phases have been assessed. These studies addressed malignancy and injury as well as repair, including fracture healing and cell/gene therapy for skeletal defects. In the joints, molecular imaging has focused on the inflammatory and tissue destructive processes that cause arthritis. As described in this review, the feasibility of applying molecular imaging to numerous areas of orthopedic research has been demonstrated and will likely result in an increase in research dedicated to this powerful strategy. Molecular imaging holds great promise in the future for preclinical orthopedic research as well as next-generation clinical musculoskeletal diagnostics.

  11. Technique development of 3D dynamic CS-EPSI for hyperpolarized 13 C pyruvate MR molecular imaging of human prostate cancer.

    Science.gov (United States)

    Chen, Hsin-Yu; Larson, Peder E Z; Gordon, Jeremy W; Bok, Robert A; Ferrone, Marcus; van Criekinge, Mark; Carvajal, Lucas; Cao, Peng; Pauly, John M; Kerr, Adam B; Park, Ilwoo; Slater, James B; Nelson, Sarah J; Munster, Pamela N; Aggarwal, Rahul; Kurhanewicz, John; Vigneron, Daniel B

    2018-03-25

    The purpose of this study was to develop a new 3D dynamic carbon-13 compressed sensing echoplanar spectroscopic imaging (EPSI) MR sequence and test it in phantoms, animal models, and then in prostate cancer patients to image the metabolic conversion of hyperpolarized [1- 13 C]pyruvate to [1- 13 C]lactate with whole gland coverage at high spatial and temporal resolution. A 3D dynamic compressed sensing (CS)-EPSI sequence with spectral-spatial excitation was designed to meet the required spatial coverage, time and spatial resolution, and RF limitations of the 3T MR scanner for its clinical translation for prostate cancer patient imaging. After phantom testing, animal studies were performed in rats and transgenic mice with prostate cancers. For patient studies, a GE SPINlab polarizer (GE Healthcare, Waukesha, WI) was used to produce hyperpolarized sterile GMP [1- 13 C]pyruvate. 3D dynamic 13 C CS-EPSI data were acquired starting 5 s after injection throughout the gland with a spatial resolution of 0.5 cm 3 , 18 time frames, 2-s temporal resolution, and 36 s total acquisition time. Through preclinical testing, the 3D CS-EPSI sequence developed in this project was shown to provide the desired spectral, temporal, and spatial 5D HP 13 C MR data. In human studies, the 3D dynamic HP CS-EPSI approach provided first-ever simultaneously volumetric and dynamic images of the LDH-catalyzed conversion of [1- 13 C]pyruvate to [1- 13 C]lactate in a biopsy-proven prostate cancer patient with full gland coverage. The results demonstrate the feasibility to characterize prostate cancer metabolism in animals, and now patients using this new 3D dynamic HP MR technique to measure k PL , the kinetic rate constant of [1- 13 C]pyruvate to [1- 13 C]lactate conversion. © 2018 International Society for Magnetic Resonance in Medicine.

  12. Molecular imaging of mental disorders

    International Nuclear Information System (INIS)

    Takahashi, Hidehiko; Suhara, Tetsuya

    2005-01-01

    Positron emission tomography (PET) techniques have made it possible to measure changes in neurochemical components in living human brain. PET can be used to investigate various brain functions such as receptors, transporters, enzymes and various biochemical pathways; therefore, it could be a powerful tool for molecular imaging of mental disorders. Since the pathophysiology of schizophrenia has been discussed with a functional alteration of dopaminergic transmission in the brain, we have focused the dopaminergic components for the research target of schizophrenia using PET. Using high affinity ligand [ 11 C]FLB 457, we found reduced D 2 receptor binding in the anterior cingulate cortex of patients with schizophrenia, and a significant negative correlation was observed between D 2 receptor binding and the positive symptom score. Subregions of interest were defined on the thalamus using individual magnetic resonance images. D 2 receptor binding was also lower in the central medial and posterior subregions of the thalamus in patients with schizophrenia. Alterations in D 2 receptor function in the extrastriatal region may underlie the positive symptoms of schizophrenia. On the other hand D 1 receptor binding was found to be lower in the prefrontal cortex and a significant negative correlation was observed between D 1 receptor binding and the negative symptom score. Abnormality of D 1 receptor function would be at the bottom of the negative symptoms and cognitive impairment of schizophrenia. Regarding the effect of antipsychotics on dopamine D 2 receptor, occupancy and it's time-course have been measured in a living body using PET. This approach can provide in vivo pharmacological evidences of antipsychotics and establish the rational therapeutic strategy. PET is a powerful tool not only in the field of brain research but also drug discovery. (author)

  13. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  14. Dynamics of molecular superrotors in an external magnetic field

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Valery

    2015-08-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  15. Dynamics of molecular superrotors in an external magnetic field

    International Nuclear Information System (INIS)

    Korobenko, Aleksey; Milner, Valery

    2015-01-01

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

  16. Chirality in molecular collision dynamics

    Science.gov (United States)

    Lombardi, Andrea; Palazzetti, Federico

    2018-02-01

    Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

  17. Molecular imaging of oncolytic viral therapy

    Directory of Open Access Journals (Sweden)

    Dana Haddad

    2014-01-01

    Full Text Available Oncolytic viruses have made their mark on the cancer world as a potential therapeutic option, with the possible advantages of reduced side effects and strengthened treatment efficacy due to higher tumor selectivity. Results have been so promising, that oncolytic viral treatments have now been approved for clinical trials in several countries. However, clinical studies may benefit from the ability to noninvasively and serially identify sites of viral targeting via molecular imaging in order to provide safety, efficacy, and toxicity information. Furthermore, molecular imaging of oncolytic viral therapy may provide a more sensitive and specific diagnostic technique to detect tumor origin and, more importantly, presence of metastases. Several strategies have been investigated for molecular imaging of viral replication broadly categorized into optical and deep tissue imaging, utilizing several reporter genes encoding for fluorescence proteins, conditional enzymes, and membrane protein and transporters. Various imaging methods facilitate molecular imaging, including computer tomography, magnetic resonance imaging, positron emission tomography, single photon emission CT, gamma-scintigraphy, and photoacoustic imaging. In addition, several molecular probes are used for medical imaging, which act as targeting moieties or signaling agents. This review will explore the preclinical and clinical use of in vivo molecular imaging of replication-competent oncolytic viral therapy.

  18. Molecular dynamics for reactions of heterogeneous catalysis

    NARCIS (Netherlands)

    Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

    1991-01-01

    An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

  19. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  20. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  1. Inorganic Nanoparticles for Multimodal Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Magdalena Swierczewska

    2011-01-01

    Full Text Available Multimodal molecular imaging can offer a synergistic improvement of diagnostic ability over a single imaging modality. Recent development of hybrid imaging systems has profoundly impacted the pool of available multimodal imaging probes. In particular, much interest has been focused on biocompatible, inorganic nanoparticle-based multimodal probes. Inorganic nanoparticles offer exceptional advantages to the field of multimodal imaging owing to their unique characteristics, such as nanometer dimensions, tunable imaging properties, and multifunctionality. Nanoparticles mainly based on iron oxide, quantum dots, gold, and silica have been applied to various imaging modalities to characterize and image specific biologic processes on a molecular level. A combination of nanoparticles and other materials such as biomolecules, polymers, and radiometals continue to increase functionality for in vivo multimodal imaging and therapeutic agents. In this review, we discuss the unique concepts, characteristics, and applications of the various multimodal imaging probes based on inorganic nanoparticles.

  2. Dynamical processes in atomic and molecular physics

    CERN Document Server

    Ogurtsov, Gennadi

    2012-01-01

    Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

  3. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  4. Molecular ions, Rydberg spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Jungen, Ch.

    2015-01-01

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

  5. Pattern recognition in molecular dynamics. [FORTRAN

    Energy Technology Data Exchange (ETDEWEB)

    Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

    1977-07-01

    An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

  6. Molecular ions, Rydberg spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  7. Current state of molecular imaging research

    International Nuclear Information System (INIS)

    Grimm, J.; Wunder, A.

    2005-01-01

    The recent years have seen significant advances in both molecular biology, allowing the identification of genes and pathways related to disease, and imaging technologies that allow for improved spatial and temporal resolution, enhanced sensitivity, better depth penetration, improved image processing, and beneficial combinations of different imaging modalities. These advances have led to a paradigm shift in the scope of diagnostic imaging. The traditional role of radiological diagnostic imaging is to define gross anatomy and structure in order to detect pathological abnormalities. Available contrast agents are mostly non-specific and can be used to image physiological processes such as changes in blood volume, flow, and perfusion but not to demonstrate pathological alterations at molecular levels. However, alterations at the anatomical-morphological level are relatively late manifestations of underlying molecular changes. Using molecular probes or markers that bind specifically to molecular targets allows for the non-invasive visualization and quantitation of biological processes such as gene expression, apoptosis, or angiogenesis at the molecular level within intact living organisms. This rapidly evolving, multidisciplinary approach, referred to as molecular imaging, promises to enable early diagnosis, can provide improved classification of stage and severity of disease, an objective assessment of treatment efficacy, and a reliable prognosis. Furthermore, molecular imaging is an important tool for the evaluation of physiological and pathophysiological processes, and for the development of new therapies. This article comprises a review of current technologies of molecular imaging, describes the development of contrast agents and various imaging modalities, new applications in specific disease models, and potential future developments. (orig.)

  8. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  9. PET-based molecular imaging in neuroscience

    International Nuclear Information System (INIS)

    Jacobs, A.H.; Heiss, W.D.; Li, H.; Knoess, C.; Schaller, B.; Kracht, L.; Monfared, P.; Vollmar, S.; Bauer, B.; Wagner, R.; Graf, R.; Wienhard, K.; Winkeler, A.; Rueger, A.; Klein, M.; Hilker, R.; Galldiks, N.; Herholz, K.; Sobesky, J.

    2003-01-01

    Positron emission tomography (PET) allows non-invasive assessment of physiological, metabolic and molecular processes in humans and animals in vivo. Advances in detector technology have led to a considerable improvement in the spatial resolution of PET (1-2 mm), enabling for the first time investigations in small experimental animals such as mice. With the developments in radiochemistry and tracer technology, a variety of endogenously expressed and exogenously introduced genes can be analysed by PET. This opens up the exciting and rapidly evolving field of molecular imaging, aiming at the non-invasive localisation of a biological process of interest in normal and diseased cells in animal models and humans in vivo. The main and most intriguing advantage of molecular imaging is the kinetic analysis of a given molecular event in the same experimental subject over time. This will allow non-invasive characterisation and ''phenotyping'' of animal models of human disease at various disease stages, under certain pathophysiological stimuli and after therapeutic intervention. The potential broad applications of imaging molecular events in vivo lie in the study of cell biology, biochemistry, gene/protein function and regulation, signal transduction, transcriptional regulation and characterisation of transgenic animals. Most importantly, molecular imaging will have great implications for the identification of potential molecular therapeutic targets, in the development of new treatment strategies, and in their successful implementation into clinical application. Here, the potential impact of molecular imaging by PET in applications in neuroscience research with a special focus on neurodegeneration and neuro-oncology is reviewed. (orig.)

  10. Wavelet Analysis for Molecular Dynamics

    Science.gov (United States)

    2015-06-01

    Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the

  11. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

  12. Nanobody: the "magic bullet" for molecular imaging?

    Science.gov (United States)

    Chakravarty, Rubel; Goel, Shreya; Cai, Weibo

    2014-01-01

    Molecular imaging involves the non-invasive investigation of biological processes in vivo at the cellular and molecular level, which can play diverse roles in better understanding and treatment of various diseases. Recently, single domain antigen-binding fragments known as 'nanobodies' were bioengineered and tested for molecular imaging applications. Small molecular size (~15 kDa) and suitable configuration of the complementarity determining regions (CDRs) of nanobodies offer many desirable features suitable for imaging applications, such as rapid targeting and fast blood clearance, high solubility, high stability, easy cloning, modular nature, and the capability of binding to cavities and difficult-to-access antigens. Using nanobody-based probes, several imaging techniques such as radionuclide-based, optical and ultrasound have been employed for visualization of target expression in various disease models. This review summarizes the recent developments in the use of nanobody-based probes for molecular imaging applications. The preclinical data reported to date are quite promising, and it is expected that nanobody-based molecular imaging agents will play an important role in the diagnosis and management of various diseases.

  13. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

    This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

  14. Molecular dynamics and diffusion a compilation

    CERN Document Server

    Fisher, David

    2013-01-01

    The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

  15. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

  16. Molecular dynamics modeling of polymer flammability

    International Nuclear Information System (INIS)

    Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

    1992-01-01

    Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

  17. First-principles molecular dynamics for metals

    International Nuclear Information System (INIS)

    Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

    1989-01-01

    A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

  18. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  19. Theory and application of quantum molecular dynamics

    CERN Document Server

    Zeng Hui Zhang, John

    1999-01-01

    This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

  20. Musashi dynamic image processing system

    International Nuclear Information System (INIS)

    Murata, Yutaka; Mochiki, Koh-ichi; Taguchi, Akira

    1992-01-01

    In order to produce transmitted neutron dynamic images using neutron radiography, a real time system called Musashi dynamic image processing system (MDIPS) was developed to collect, process, display and record image data. The block diagram of the MDIPS is shown. The system consists of a highly sensitive, high resolution TV camera driven by a custom-made scanner, a TV camera deflection controller for optimal scanning, which adjusts to the luminous intensity and the moving speed of an object, a real-time corrector to perform the real time correction of dark current, shading distortion and field intensity fluctuation, a real time filter for increasing the image signal to noise ratio, a video recording unit and a pseudocolor monitor to realize recording in commercially available products and monitoring by means of the CRTs in standard TV scanning, respectively. The TV camera and the TV camera deflection controller utilized for producing still images can be applied to this case. The block diagram of the real-time corrector is shown. Its performance is explained. Linear filters and ranked order filters were developed. (K.I.)

  1. Nonadiabatic electron wavepacket dynamics behind molecular autoionization

    Science.gov (United States)

    Matsuoka, Takahide; Takatsuka, Kazuo

    2018-01-01

    A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

  2. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  3. Fluorescence based molecular in vivo imaging

    International Nuclear Information System (INIS)

    Ebert, Bernd

    2008-01-01

    Molecular imaging represents a modern research area that allows the in vivo study of molecular biological process kinetics using appropriate probes and visualization methods. This methodology may be defined- apart from the contrast media injection - as non-abrasive. In order to reach an in vivo molecular process imaging as accurate as possible the effects of the used probes on the biological should not be too large. The contrast media as important part of the molecular imaging can significantly contribute to the understanding of molecular processes and to the development of tailored diagnostics and therapy. Since more than 15 years PTB is developing optic imaging systems that may be used for fluorescence based visualization of tissue phantoms, small animal models and the localization of tumors and their predecessors, and for the early recognition of inflammatory processes in clinical trials. Cellular changes occur during many diseases, thus the molecular imaging might be of importance for the early diagnosis of chronic inflammatory diseases. Fluorescent dyes can be used as unspecific or also as specific contrast media, which allow enhanced detection sensitivity

  4. Dynamic signature of molecular association in methanol

    International Nuclear Information System (INIS)

    Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

    2016-01-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

  5. Molecular and parametric imaging with iron oxides

    International Nuclear Information System (INIS)

    Matuszewski, L.; Bremer, C.; Tombach, B.; Heindel, W.

    2007-01-01

    Superparamagnetic iron oxide (SPIO) contrast agents, clinically established for high resolution magnetic resonance imaging of reticuloendothelial system containing anatomical structures, can additionally be exploited for the non-invasive characterization and quantification of pathology down to the molecular level. In this context, SPIOs can be applied for non-invasive cell tracking, quantification of tissue perfusion and target specific imaging, as well as for the detection of gene expression. This article provides an overview of new applications for clinically approved iron oxides as well of new, modified SPIO contrast agents for parametric and molecular imaging. (orig.) [de

  6. Molecular Imaging Probe Development using Microfluidics

    Science.gov (United States)

    Liu, Kan; Wang, Ming-Wei; Lin, Wei-Yu; Phung, Duy Linh; Girgis, Mark D.; Wu, Anna M.; Tomlinson, James S.; Shen, Clifton K.-F.

    2012-01-01

    In this manuscript, we review the latest advancement of microfluidics in molecular imaging probe development. Due to increasing needs for medical imaging, high demand for many types of molecular imaging probes will have to be met by exploiting novel chemistry/radiochemistry and engineering technologies to improve the production and development of suitable probes. The microfluidic-based probe synthesis is currently attracting a great deal of interest because of their potential to deliver many advantages over conventional systems. Numerous chemical reactions have been successfully performed in micro-reactors and the results convincingly demonstrate with great benefits to aid synthetic procedures, such as purer products, higher yields, shorter reaction times compared to the corresponding batch/macroscale reactions, and more benign reaction conditions. Several ‘proof-of-principle’ examples of molecular imaging probe syntheses using microfluidics, along with basics of device architecture and operation, and their potential limitations are discussed here. PMID:22977436

  7. High sensitivity optical molecular imaging system

    Science.gov (United States)

    An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

    2018-02-01

    Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

  8. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  9. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  10. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  11. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  12. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  13. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  14. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  15. Catalysis and communication in dynamic molecular networks

    NARCIS (Netherlands)

    Fanlo Virgos, Hugo

    2015-01-01

    The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

  16. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  17. Has molecular imaging delivered to drug development?

    Science.gov (United States)

    Murphy, Philip S.; Patel, Neel; McCarthy, Timothy J.

    2017-10-01

    Pharmaceutical research and development requires a systematic interrogation of a candidate molecule through clinical studies. To ensure resources are spent on only the most promising molecules, early clinical studies must understand fundamental attributes of the drug candidate, including exposure at the target site, target binding and pharmacological response in disease. Molecular imaging has the potential to quantitatively characterize these properties in small, efficient clinical studies. Specific benefits of molecular imaging in this setting (compared to blood and tissue sampling) include non-invasiveness and the ability to survey the whole body temporally. These methods have been adopted primarily for neuroscience drug development, catalysed by the inability to access the brain compartment by other means. If we believe molecular imaging is a technology platform able to underpin clinical drug development, why is it not adopted further to enable earlier decisions? This article considers current drug development needs, progress towards integration of molecular imaging into studies, current impediments and proposed models to broaden use and increase impact. This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.

  18. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    Directory of Open Access Journals (Sweden)

    Dirk-Sören Lühmann

    2015-08-01

    Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  19. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  20. Dynamical quenching of tunneling in molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

    José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

    2015-12-15

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

  1. Dynamical quenching of tunneling in molecular magnets

    International Nuclear Information System (INIS)

    José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

    2015-01-01

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation

  2. Molecular nuclear imaging for targeting and trafficking

    International Nuclear Information System (INIS)

    Bom, Hee Seung; Min, Jung Jun; Jeong, Hwan-Jeong

    2006-01-01

    Noninvasive molecular targeting in living subjects is highly demanded for better understanding of such diverse topics as the efficient delivery of drugs, genes, or radionuclides for the diagnosis or treatment of diseases. Progress in molecular biology, genetic engineering and polymer chemistry provides various tools to target molecules and cells in vivo. We used chitosan as a polymer, and 99m Tc as a radionuclide. We developed 99m Tc-galactosylated chitosan to target asialoglycoprotein receptors for nuclear imaging. We also developed 99m Tc-HYNIC-chitosan-transferrin to target inflammatory cells, which was more effective than 67 Ga-citrate for imaging inflammatory lesions. For an effective delivery of molecules, a longer circulation time is needed. We found that around 10% PEGylation was most effective to prolong the circulation time of liposomes for nuclear imaging of 99m Tc-HMPAO-labeled liposomes in rats. Using various characteristics of molecules, we can deliver drugs into targets more effectively. We found that 99m Tc-labeled biodegradable pullulan-derivatives are retained in tumor tissue in response to extracellular ion-strength. For the trafficking of various cells or bacteria in an intact animal, we used optical imaging techniques or radiolabeled cells. We monitored tumor-targeting bacteria by bioluminescent imaging techniques, dentritic cells by radiolabeling and neuronal stem cells by sodium-iodide symporter reporter gene imaging. In summary, we introduced recent achievements of molecular nuclear imaging technologies in targeting receptors for hepatocyte or inflammatory cells and in trafficking bacterial, immune and stem cells using molecular nuclear imaging techniques

  3. A review of molecular imaging studies reaching the clinical stage

    International Nuclear Information System (INIS)

    Wong, Franklin C.; Kim, E. Edmund

    2009-01-01

    The practice of molecular imaging in the clinics is examined across various imaging modalities to assess the current status of clinical molecular imaging. The various physiologic and scientific bases of clinical molecular imaging are surveyed to assess the possibilities and opportunities for the deployment of the different imaging modalities in the near future. The requisites for successful candidate(s) of clinical molecular imaging are reviewed for future development.

  4. Orthonormal Wavelet Bases for Quantum Molecular Dynamics

    International Nuclear Information System (INIS)

    Tymczak, C.; Wang, X.

    1997-01-01

    We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

  5. Geocoronal imaging with Dynamics Explorer

    Science.gov (United States)

    Rairden, R. L.; Frank, L. A.; Craven, J. D.

    1986-01-01

    The ultraviolet photometer of the University of Iowa spin-scan auroral imaging instrumentation on board Dynamics Explorer-1 has returned numerous hydrogen Lyman alpha images of the geocorona from altitudes of 570 km to 23,300 km (1.09 R sub E to 4.66 R sub E geocentric radial distance). The hydrogen density gradient is shown by a plot of the zenith intensities throughout this range, which decrease to near celestial background values as the spacecraft approaches apogee. Characterizing the upper geocorona as optically thin (single-scattering), the zenith intensity is converted directly to vertical column density. This approximation loses its validity deeper in the geocorona, where the hydrogen is demonstrated to be optically thick in that there is no Lyman alpha limb brightening. Further study of the geocoronal hydrogen distribution will require computer modeling of the radiative transfer.

  6. In Vivo Imaging of Molecularly Targeted Phage

    Directory of Open Access Journals (Sweden)

    Kimberly A. Kelly

    2006-12-01

    Full Text Available Rapid identification of in vivo affinity ligands would have far-reaching applications for imaging specific molecular targets, in vivo systems imaging, and medical use. We have developed a high-throughput method for identifying and optimizing ligands to map and image biologic targets of interest in vivo. We directly labeled viable phage clones with far-red fluorochromes and comparatively imaged them in vivo by multichannel fluorescence ratio imaging. Using Secreted Protein Acidic and Rich in Cysteine (osteonectin and vascular cell adhesion molecule-1 as model targets, we show that: 1 fluorescently labeled phage retains target specificity on labeling; 2 in vivo distribution can be quantitated (detection thresholds of ~ 300 phage/mm3 tissue throughout the entire depth of the tumor using fluorescent tomographic imaging; and 3 fluorescently labeled phage itself can serve as a replenishable molecular imaging agent. The described method should find widespread application in the rapid in vivo discovery and validation of affinity ligands and, importantly, in the use of fluorochrome-labeled phage clones as in vivo imaging agents.

  7. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    International Nuclear Information System (INIS)

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-01-01

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  8. Excited-state molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Pratt, S.T.

    1995-01-01

    This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

  9. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  10. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  11. Molecular quantum dynamics. From theory to applications

    International Nuclear Information System (INIS)

    Gatti, Fabien

    2014-01-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

  12. Molecular quantum dynamics. From theory to applications

    Energy Technology Data Exchange (ETDEWEB)

    Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

    2014-09-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

  13. Molecular Imaging in Nanotechnology and Theranostics.

    Science.gov (United States)

    Andreou, Chrysafis; Pal, Suchetan; Rotter, Lara; Yang, Jiang; Kircher, Moritz F

    2017-06-01

    The fields of biomedical nanotechnology and theranostics have enjoyed exponential growth in recent years. The "Molecular Imaging in Nanotechnology and Theranostics" (MINT) Interest Group of the World Molecular Imaging Society (WMIS) was created in order to provide a more organized and focused forum on these topics within the WMIS and at the World Molecular Imaging Conference (WMIC). The interest group was founded in 2015 and was officially inaugurated during the 2016 WMIC. The overarching goal of MINT is to bring together the many scientists who work on molecular imaging approaches using nanotechnology and those that work on theranostic agents. MINT therefore represents scientists, labs, and institutes that are very diverse in their scientific backgrounds and areas of expertise, reflecting the wide array of materials and approaches that drive these fields. In this short review, we attempt to provide a condensed overview over some of the key areas covered by MINT. Given the breadth of the fields and the given space constraints, we have limited the coverage to the realm of nanoconstructs, although theranostics is certainly not limited to this domain. We will also focus only on the most recent developments of the last 3-5 years, in order to provide the reader with an intuition of what is "in the pipeline" and has potential for clinical translation in the near future.

  14. Towards molecular imaging by means of MRI

    NARCIS (Netherlands)

    Norek, M.

    2008-01-01

    The work presented in the thesis is focused on the design of highly efficient contrast agents for molecular imaging by means of MRI based on the detailed physical characterization of the given material. Specifically, attention is paid on the development of contrast agents for magnetic fields higher

  15. Molecular Imaging in Schizophrenia Spectrum Disorders

    NARCIS (Netherlands)

    Klein, H.C.; Doorduin, J.; van Berckel, B.N.M.

    2014-01-01

    In this chapter, we aim to shed light on the schizophrenia spectrum disorders using molecular imaging. Schizophrenia spectrum disorders consist primarily of the disorders with full-blown psychosis in their course and are grouped in the DSM-IV category of schizophrenia and other psychotic disorders.

  16. Molecular Dynamics with Helical Periodic Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  17. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  18. Quantitative assessment of dynamic PET imaging data in cancer imaging.

    Science.gov (United States)

    Muzi, Mark; O'Sullivan, Finbarr; Mankoff, David A; Doot, Robert K; Pierce, Larry A; Kurland, Brenda F; Linden, Hannah M; Kinahan, Paul E

    2012-11-01

    Clinical imaging in positron emission tomography (PET) is often performed using single-time-point estimates of tracer uptake or static imaging that provides a spatial map of regional tracer concentration. However, dynamic tracer imaging can provide considerably more information about in vivo biology by delineating both the temporal and spatial pattern of tracer uptake. In addition, several potential sources of error that occur in static imaging can be mitigated. This review focuses on the application of dynamic PET imaging to measuring regional cancer biologic features and especially in using dynamic PET imaging for quantitative therapeutic response monitoring for cancer clinical trials. Dynamic PET imaging output parameters, particularly transport (flow) and overall metabolic rate, have provided imaging end points for clinical trials at single-center institutions for years. However, dynamic imaging poses many challenges for multicenter clinical trial implementations from cross-center calibration to the inadequacy of a common informatics infrastructure. Underlying principles and methodology of PET dynamic imaging are first reviewed, followed by an examination of current approaches to dynamic PET image analysis with a specific case example of dynamic fluorothymidine imaging to illustrate the approach. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Nonequilibrium molecular dynamics theory, algorithms and applications

    CERN Document Server

    Todd, Billy D

    2017-01-01

    Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

  20. Extended Lagrangian Excited State Molecular Dynamics.

    Science.gov (United States)

    Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

    2018-02-13

    An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

  1. Connotation and category of functional-molecular imaging

    International Nuclear Information System (INIS)

    Li Tianran; Tian Jiahe

    2007-01-01

    Function and molecular lmaging represent medical imaging' s direction. The review article introduce function and molecular's concept and category and its characteristic. Comparing with traditionary classics radiology, function and molecular imaging have many features, such as micro-mount and specificity and quantitative. There are many technology about function and molecular imaging. Function and molecular imaging is important ingredient of modern medical and play a considerable role. (authors)

  2. Molecular photoacoustic imaging of follicular thyroid carcinoma

    DEFF Research Database (Denmark)

    Levi, Jelena; Kothapalli, Sri-Rajashekar; Bohndiek, Sarah

    2013-01-01

    in living mice optically, observing the increase in Alexa750 fluorescence, and photoacoustically, using a dual wavelength imaging method. Results Active forms of both MMP2 and MMP-9 enzymes were found in FTC133 tumor homogenates, with MMP-9 detected in greater amounts. The molecular imaging agent......Purpose To evaluate the potential of targeted photoacoustic imaging as a non-invasive method for detection of follicular thyroid carcinoma. Experimental Design We determined the presence and activity of two members of matrix metalloproteinase family (MMP), MMP-2 and MMP-9, suggested as biomarkers...... for malignant thyroid lesions, in FTC133 thyroid tumors subcutaneously implanted in nude mice. The imaging agent used to visualize tumors was MMP activatable photoacoustic probe, Alexa750-CXeeeeXPLGLAGrrrrrXK-BHQ3. Cleavage of the MMP activatable agent was imaged after intratumoral and intravenous injections...

  3. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  4. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  5. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.; Vashishta, P.

    1983-01-01

    Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

  6. Molecular Imaging and nuclear medicine: expectations and requirements

    International Nuclear Information System (INIS)

    Rollo, F.D.

    2003-01-01

    Molecular Imaging with Nuclear Medicine offers earlier, more accurate and more specific diagnosis, as well as targeted molecular therapy, providing significant improvements in clinical outcomes. (orig.)

  7. High dynamic range coding imaging system

    Science.gov (United States)

    Wu, Renfan; Huang, Yifan; Hou, Guangqi

    2014-10-01

    We present a high dynamic range (HDR) imaging system design scheme based on coded aperture technique. This scheme can help us obtain HDR images which have extended depth of field. We adopt Sparse coding algorithm to design coded patterns. Then we utilize the sensor unit to acquire coded images under different exposure settings. With the guide of the multiple exposure parameters, a series of low dynamic range (LDR) coded images are reconstructed. We use some existing algorithms to fuse and display a HDR image by those LDR images. We build an optical simulation model and get some simulation images to verify the novel system.

  8. Dynamic CT myocardial perfusion imaging

    International Nuclear Information System (INIS)

    Caruso, Damiano; Eid, Marwen; Schoepf, U. Joseph; Jin, Kwang Nam; Varga-Szemes, Akos; Tesche, Christian; Mangold, Stefanie

    2016-01-01

    Highlights: • CT myocardial perfusion provides functional assessment of the myocardium. • CCTA is limited in determining the hemodynamic significance of coronary stenosis. • CT-MPI can accurately detect hemodynamically significant coronary artery stenosis. - Abstract: Non-invasive cardiac imaging has rapidly evolved during the last decade due to advancements in CT based technologies. Coronary CT angiography has been shown to reliably assess coronary anatomy and detect high risk coronary artery disease. However, this technique is limited to anatomical assessment, thus non-invasive techniques for functional assessment of the heart are necessary. CT myocardial perfusion is a new CT based technique that provides functional assessment of the myocardium and allows for a comprehensive assessment of coronary artery disease with a single modality when combined with CTA. This review aims to discuss dynamic CT myocardial perfusion as a new technique in the assessment of CAD.

  9. Dynamic CT myocardial perfusion imaging

    Energy Technology Data Exchange (ETDEWEB)

    Caruso, Damiano [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Department of Radiological Sciences, Oncological and Pathological Sciences, University of Rome “Sapienza”, Latina (Italy); Eid, Marwen [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Schoepf, U. Joseph, E-mail: schoepf@musc.edu [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, SC (United States); Jin, Kwang Nam [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Department of Radiology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul (Korea, Republic of); Varga-Szemes, Akos [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Tesche, Christian [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Department of Cardiology and Intensive Care Medicine, Heart Center Munich-Bogenhausen, Munich (Germany); Mangold, Stefanie [Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC (United States); Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen (Germany); and others

    2016-10-15

    Highlights: • CT myocardial perfusion provides functional assessment of the myocardium. • CCTA is limited in determining the hemodynamic significance of coronary stenosis. • CT-MPI can accurately detect hemodynamically significant coronary artery stenosis. - Abstract: Non-invasive cardiac imaging has rapidly evolved during the last decade due to advancements in CT based technologies. Coronary CT angiography has been shown to reliably assess coronary anatomy and detect high risk coronary artery disease. However, this technique is limited to anatomical assessment, thus non-invasive techniques for functional assessment of the heart are necessary. CT myocardial perfusion is a new CT based technique that provides functional assessment of the myocardium and allows for a comprehensive assessment of coronary artery disease with a single modality when combined with CTA. This review aims to discuss dynamic CT myocardial perfusion as a new technique in the assessment of CAD.

  10. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  11. Optical Molecular Imaging Frontiers in Oncology: The Pursuit of Accuracy and Sensitivity

    Directory of Open Access Journals (Sweden)

    Kun Wang

    2015-09-01

    Full Text Available Cutting-edge technologies in optical molecular imaging have ushered in new frontiers in cancer research, clinical translation, and medical practice, as evidenced by recent advances in optical multimodality imaging, Cerenkov luminescence imaging (CLI, and optical image-guided surgeries. New abilities allow in vivo cancer imaging with sensitivity and accuracy that are unprecedented in conventional imaging approaches. The visualization of cellular and molecular behaviors and events within tumors in living subjects is improving our deeper understanding of tumors at a systems level. These advances are being rapidly used to acquire tumor-to-tumor molecular heterogeneity, both dynamically and quantitatively, as well as to achieve more effective therapeutic interventions with the assistance of real-time imaging. In the era of molecular imaging, optical technologies hold great promise to facilitate the development of highly sensitive cancer diagnoses as well as personalized patient treatment—one of the ultimate goals of precision medicine.

  12. Ethical and regulatory problems of molecular imaging

    International Nuclear Information System (INIS)

    Jeong, Jae Min

    2004-01-01

    As a molecular imaging is the most up-to-date technology in nuclear medicine, it has complicate ethical and regulatory problems. For animal experiment, we have to follow institutional animal care committee. For clinical experiment, we have to get approval of Institutional Review Board according to Helsinki declaration. In addition, approval from Korea Food and Drug Administration (KFDA) is essential for manufacturing and commercialization. However, too much regulation would suppress development of new technology, which would result in the loss of national competitive power. In addition, most new radioactive ligands for molecular imaging are administered to human at sub-pharmacological and sub-toxicological level. In conclusion, a balanced regulation is essential for the safety of clinical application and development of new technology

  13. Molecular Dynamics: New Frontier in Personalized Medicine.

    Science.gov (United States)

    Sneha, P; Doss, C George Priya

    2016-01-01

    The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

  14. Dynamic MR imaging of pancreatic cancer

    International Nuclear Information System (INIS)

    Akaki, Shiro; Kohno, Yoshihiro; Gohbara, Hideo

    1994-01-01

    Dynamic MRI was performed on 21 patients with pancreatic duct cell carcinoma. Turbo-FLASH or FLASH3D was performed immediately following rapid bolus injection of gadopentetate dimeglumine, and these FLASH images and conventional spin echo images were evaluated about detectability of the lesion. All images were classified into three groups of detectability of the lesion ; good, fair, and poor. On T 1 weighted image, 23% of cases were 'good' and 48% were evaluated as 'fair'. On the other hand, on dynamic MRI, 62% of cases were 'good' and 33% of cases were evaluated as 'fair'. Both T 2 weighted image and enhanced T 1 weighted image were not useful for depiction of the lesion. Direct comparison between T 1 weighted image and dynamic MRI was also done. In 55% of cases, dynamic MRI was superior to T 1 weighted image and in 40% of cases, dynamic MRI was equal to T 1 weighted image. Thus, dynamic MRI was superior to conventional spin echo images for detection of duct cell carcinoma. In 17 patients of duct cell carcinoma who underwent FLASH3D, contrast/noise ratio (CNR) was calculated before and after injection of gadopentetate dimeglumine. The absolute value of CNR became significantly larger by injection of contrast material. In nine resectable pancreatic carcinomas, two cases of INF α and two cases of medullary type were well depicted. It was concluded that dynamic MRI was useful for evaluation of pancreatic carcinoma. (author)

  15. Parallelization of quantum molecular dynamics simulation code

    International Nuclear Information System (INIS)

    Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

    1998-02-01

    A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

  16. Lipid Configurations from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek

    2018-01-01

    of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...

  17. Molecular dynamics studies of actinide nitrides

    International Nuclear Information System (INIS)

    Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

    2004-01-01

    The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)

  18. Viscosity calculations at molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kirova, E M; Norman, G E

    2015-01-01

    Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)

  19. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  20. Molecular dynamics of surfactant protein C

    DEFF Research Database (Denmark)

    Ramírez, Eunice; Santana, Alberto; Cruz, Anthony

    2006-01-01

    Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...

  1. Dynamic MR imaging in the musculoskeletal system

    International Nuclear Information System (INIS)

    Hedlund, L.; Vogler, J.; Utz, J.A.; Herfkens, R.J.; Martinez, S.; Urbaniak, J.; Evans, A.

    1986-01-01

    Many joint disorders are related to movement, and lack of dynamic imaging has thus far been a limitation of MR imaging. A recently developed dynamic MR imaging technique utilizing a gradient refocused echo (TE = 12 msec, TR = 21 msec) coupled to a physiologic trigger allows dynamic images of the moving joint to be obtained. Controlled joint articulation is produced using an air-driven nonmagnetic device. Imaging of the wrist by this technique demonstrated the dynamic motion of the carpal rows. The method displays cartilage with more sensitivity than does conventional MR imaging; thus, ligamentous and triangular cartilage alignment could be evaluated during motion. In the wrist, potential applications include imaging of carpal instability syndromes, ligamentous interruption, and tears of the triangular cartilage

  2. Molecular dynamics in high electric fields

    International Nuclear Information System (INIS)

    Apostol, M.; Cune, L.C.

    2016-01-01

    Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

  3. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

    Science.gov (United States)

    Gilad, Assaf A; Shapiro, Mikhail G

    2017-06-01

    Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

  4. Classical molecular dynamics simulation of nuclear fuels

    International Nuclear Information System (INIS)

    Devanathan, R.; Krack, M.; Bertolus, M.

    2015-01-01

    Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

  5. Dynamic MR imaging of the musculoskeletal system

    International Nuclear Information System (INIS)

    Shah, A.S.; Hylton, H.; Hentz, V.R.; Schattner, P.

    1991-01-01

    This paper reports on dynamic MR imaging which is an MR technique that allows imaging of the musculoskeletal system in motion. Current methods for observing the articulation of muscles and joints are limited to acquisition of stationary images at different spatial orientations. These images are then replayed from computer memory to simulate motion. Unlike stationary acquisition, dynamic MR imaging allows the volume of interest to be subjected to motion and dynamic stress, which is important for detecting stress-induced pathology. To demonstrate the utility of dynamic MR imaging, a system for imaging a moving wrist has been developed. The system consists of apparatus capable of providing simultaneous radialulnar deviation and flexion-extension, and hardware for system control and acquisition gating. The apparatus is mounted on the patient bed and is transferable to a variety of standard clinical MR imaging systems. Images were obtained during motion, and the ability of dynamic MR imaging to accurately image the moving wrist with very little motion artifact was demonstrated

  6. Image reconstruction of dynamic infrared single-pixel imaging system

    Science.gov (United States)

    Tong, Qi; Jiang, Yilin; Wang, Haiyan; Guo, Limin

    2018-03-01

    Single-pixel imaging technique has recently received much attention. Most of the current single-pixel imaging is aimed at relatively static targets or the imaging system is fixed, which is limited by the number of measurements received through the single detector. In this paper, we proposed a novel dynamic compressive imaging method to solve the imaging problem, where exists imaging system motion behavior, for the infrared (IR) rosette scanning system. The relationship between adjacent target images and scene is analyzed under different system movement scenarios. These relationships are used to build dynamic compressive imaging models. Simulation results demonstrate that the proposed method can improve the reconstruction quality of IR image and enhance the contrast between the target and the background in the presence of system movement.

  7. The 2011 Dynamics of Molecular Collisions Conference

    Energy Technology Data Exchange (ETDEWEB)

    Nesbitt, David J. [JILA, NIST

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  8. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  9. Molecular Imaging with Activatable Reporter Systems

    Directory of Open Access Journals (Sweden)

    Gang Niu, Xiaoyuan Chen

    2012-01-01

    Full Text Available Molecular imaging is a newly emerged multiple disciplinary field that aims to visualize, characterize and quantitatively measure biological processes at cellular and molecular levels in humans and other living systems. A reporter gene is a piece of DNA encoding reporter protein, which presents as a readily measurable phenotype that can be distinguished easily from the background of endogenous protein. After being transferred into cells of organ systems (transgenes, the reporter gene can be utilized to visualize transcriptional and posttranscriptional regulation of gene expression, protein-protein interactions, or trafficking of proteins or cells in living subjects. Herein, we review previous classification of reporter genes and regroup the reporter gene based imaging as basic, inducible and activatable, based on the regulation of reporter gene transcription and post-translational modification of reporter proteins. We then focus on activatable reporters, in which the signal can be activated at the posttranslational level for visualizing protein-protein interactions, protein phosphorylation or tertiary structure changes. The applications of several types of activatable reporters will also be summarized. We conclude that activatable reporter imaging can benefit both basic biomedical research and drug development.

  10. Dynamic MR imaging of pituitary adenoma

    International Nuclear Information System (INIS)

    Miki, Yukio; Nishizawa, Sadahiko; Kuroda, Yasumasa; Keyaki, Atsushi; Nabeshima, Sachio; Kawamura, Junichiro; Matsuo, Michimasa

    1990-01-01

    The authors performed serial dynamic MR imaging in patients with 10 normal pituitary and 21 pituitary adenoma utilizing spin-echo sequence with a very short repetition time (SE 100/15) every minute immediately after a bolus injection of Gd-DTPA. Usual T 1 -weighted images (SE 600/15) were also obtained before and after the dynamic study. Pituitary adenomas included 10 adenomas confirmed by surgery, 4 adenomas confirmed by biologic data, and 7 postoperative adenomas. Out of 10 patients who underwent surgery after dynamic MRI, 9 patients underwent postoperative dynamic MRI. In normal patients, the pituitary gland was markedly enhanced on the early-phase images of the dynamic study, followed by gradual decrease of intensity throughout the dynamic study. In cases of microadenomas, the contrast between the normal pituitary gland and adenoma is better than that on the usual T 1 -weighted images by marked enhancement of the normal pituitary gland. Dynamic images clearly showed the residual normal pituitary glands in all cases of macroadenoma larger than 15 mm in diameter, whereas usual contrast-enhanced images showed the normal pituitary gland only in one case. In all patients who underwent both preoperative and postoperative dynamic MRI, postoperative dynamic MRI showed the normal pituitary glands which are markedly enhanced on the early-phase images in the sites which correspond to the preoperative dynamic study. The normal residual anterior gland was also visualized in four out of 7 patients who received only postoperative dynamic MRI. Dynamic MRI is a strong diagnostic modality for visualizing microadenoma and for visualizing the normal pituitary gland in cases of preoperative and postoperative macroadenoma. (author)

  11. Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

    Science.gov (United States)

    Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

    2015-05-01

    Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

  12. Application of Deep Learning in Automated Analysis of Molecular Images in Cancer: A Survey

    Science.gov (United States)

    Xue, Yong; Chen, Shihui; Liu, Yong

    2017-01-01

    Molecular imaging enables the visualization and quantitative analysis of the alterations of biological procedures at molecular and/or cellular level, which is of great significance for early detection of cancer. In recent years, deep leaning has been widely used in medical imaging analysis, as it overcomes the limitations of visual assessment and traditional machine learning techniques by extracting hierarchical features with powerful representation capability. Research on cancer molecular images using deep learning techniques is also increasing dynamically. Hence, in this paper, we review the applications of deep learning in molecular imaging in terms of tumor lesion segmentation, tumor classification, and survival prediction. We also outline some future directions in which researchers may develop more powerful deep learning models for better performance in the applications in cancer molecular imaging. PMID:29114182

  13. Neutron imaging for inertial confinement fusion and molecular optic imaging

    International Nuclear Information System (INIS)

    Delage, O.

    2010-01-01

    Scientific domains that require imaging of micrometric/nano-metric objects are dramatically increasing (Plasma Physics, Astrophysics, Biotechnology, Earth Sciences...). Difficulties encountered in imaging smaller and smaller objects make this research area more and more challenging and in constant evolution. The two scientific domains, through which this study has been led, are the neutron imaging in the context of the inertial confinement fusion and the fluorescence molecular imaging. Work presented in this thesis has two main objectives. The first one is to describe the instrumentation characteristics that require such imagery and, relatively to the scientific domains considered, identify parameters likely to optimize the imaging system accuracy. The second one is to present the developed data analysis and reconstruction methods able to provide spatial resolution adapted to the size of the observed object. Similarities of numerical algorithms used in these two scientific domains, which goals are quiet different, show how micrometric/nano-metric object imaging is a research area at the border of a large number of scientific disciplines. (author)

  14. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp; Tchipev, Nikola

    2012-01-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

  15. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  16. Molecular imaging with targeted contrast ultrasound.

    Science.gov (United States)

    Piedra, Mark; Allroggen, Achim; Lindner, Jonathan R

    2009-01-01

    Molecular imaging with contrast-enhanced ultrasound uses targeted microbubbles that are retained in diseased tissue. The resonant properties of these microbubbles produce acoustic signals in an ultrasound field. The microbubbles are targeted to diseased tissue by using certain chemical constituents in the microbubble shell or by attaching disease-specific ligands such as antibodies to the microbubble. In this review, we discuss the applications of this technique to pathological states in the cerebrovascular system including atherosclerosis, tumor angiogenesis, ischemia, intravascular thrombus, and inflammation. Copyright 2009 S. Karger AG, Basel.

  17. Molecular imaging in Libman-Sacks endocarditis

    DEFF Research Database (Denmark)

    Dahl, Anders; Schaadt, Bente K; Santoni-Rugiu, Eric

    2015-01-01

    cardiothoracic surgery and pathologic examinations showed characteristic morphology of Libman-Sacks vegetations. All microbiological examinations including blood cultures, microscopy, culture and 16s PCR of the valve were negative and the diagnosis of Libman-Sacks endocarditis was convincing. It is difficult...... to distinguish Libman-Sacks endocarditis from culture-negative infective endocarditis (IE). Molecular imaging techniques are being used increasingly in cases of suspected IE but no studies have previously reported the use in patients with Libman-Sacks endocarditis. In the present case, (18)F-FDG-PET-CT clearly...

  18. Functional histology of tumors as a basis of molecular imaging

    International Nuclear Information System (INIS)

    Ljungkvist, A.S.; Bussink, J.; Rijken, P.F.; Van Der Kogel, A.; Kaanders, J.H.

    2003-01-01

    The aim of this study was to characterize the various elements of the microenvironment and their interrelationships by quantitative image analysis. Tumor cell proliferation, hypoxia, and apoptosis are detected by immunohistochemical methods, and mapped in relation to the vasculature. This allows quantitative relationships to be measured in the context of tissue structure. Guided by e.g., gene expression profiles for hypoxia induced-genes, several molecular markers of tumor hypoxia were identified and are immunohistochemically detectable. We have thus far concentrated on the glucose transporters glut-1 and glut-3, as well as a pH-regulating enzyme, carbonic anhydrase IX. The extent and distribution of hypoxia is assessed by administering nitroimidazole-based markers such as pimonidazole, that can be detected immunohistochemically. Multiple hypoxia markers (CCI-103F, pimonidazole) can be used to study the effects of modifiers of perfusion or oxygenation on the distribution and dynamics of hypoxic cells in the same tumor. Proliferating cells are detected by thymidine analogues. Apoptotic cells are imaged by TUNEL and caspase-3 detection. In xenografted human tumors, examples of the use of quantitative imaging of hypoxia and proliferation are the study of reoxygenation after irradiation, or the investigation of the lifespan and dynamics of hypoxic cell populations over time. Perturbation of the microenvironment after cytotoxic treatments has been investigated by co-registration of the various markers, e.g. after treatment with the hypoxic cytotoxin tirapazamine. The combination of well-timed administration of external markers of hypoxia and proliferation with the detection of intrinsic molecular markers followed by quantitative image-registration yields a comprehensive view of the dynamics of the microenvironment in individual tumors

  19. Molecular imaging of apoptosis in cancer

    International Nuclear Information System (INIS)

    Hakumaeki, Juhana M.; Liimatainen, Timo

    2005-01-01

    Apoptosis plays an important role in cancer. Mechanisms hindering its action are implicated in a number of malignancies. Also, the induction of apoptosis plays a pivotal role in non-surgical cancer treatment regimes such as irradiation, chemotherapy, or hormones. Recent advanced in imaging science have made it now possible for us to detect and visualize previously inaccessible and even unrecognized biological phenomena in cells and tissue undergoing apoptosis in vivo. Not only are these imaging techniques painting an intriguing picture of the spatiotemporal characteristics and metabolic and biophysical of apoptosis in situ, but they are expected to have an ever increasing impact in preclinical testing and design of new anticancer agents as well. Rapid and accurate visualization of apoptotic response in the clinical settings can also be of significant diagnostic and prognostic worth. With the advent of molecular medicine and patient-tailored treatment options and therapeutic agents, such monitoring techniques are becoming paramount

  20. Molecular dynamics simulation of laser shock phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).

    2001-10-01

    Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)

  1. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  2. Nonequilibrium molecular dynamics: The first 25 years

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments

  3. Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Cedrix J. Dongmo Foumthuim

    2018-01-01

    Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.

  4. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

    Science.gov (United States)

    Armen, Roger S; Chen, Jianhan; Brooks, Charles L

    2009-10-13

    Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

  5. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  6. Molecular beam studies of reaction dynamics

    International Nuclear Information System (INIS)

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation

  7. A molecular dynamics approach to barrodiffusion

    Science.gov (United States)

    Cooley, James; Marciante, Mathieu; Murillo, Michael

    2016-10-01

    Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

  8. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  9. Bioresponsive probes for molecular imaging: concepts and in vivo applications

    NARCIS (Netherlands)

    Duijnhoven, S.M. van; Robillard, M.S.; Langereis, S.; Grull, H.

    2015-01-01

    Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of

  10. Bioresponsive probes for molecular imaging : Concepts and in vivo applications

    NARCIS (Netherlands)

    van Duijnhoven, S.M.J.; Robillard, M.S.; Langereis, S.; Grüll, H.

    2015-01-01

    Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of

  11. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-01

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  12. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  13. [Molecular imaging; current status and future prospects in USA].

    Science.gov (United States)

    Kobayashi, Hisataka

    2007-02-01

    The goal of this review is to introduce the definition, current status, and future prospects of the molecular imaging, which has recently been a hot topic in medicine and the biological science in USA. In vivo imaging methods to visualize the molecular events and functions in organs or animals/humans are overviewed and discussed especially in combinations of imaging modalities (machines) and contrast agents(chemicals) used in the molecular imaging. Next, the close relationship between the molecular imaging and the nanotechnology, an important part of nanomedicine, is stressed from the aspect of united multidisciplinary sciences such as physics, chemistry, biology, and medicine.

  14. Magnetic Resonance Imaging (MRI): Dynamic Pelvic Floor

    Science.gov (United States)

    ... to a CD or uploaded to a digital cloud server. Dynamic pelvic floor MRI provides detailed pictures ... with you. top of page What are the benefits vs. risks? Benefits MRI is a noninvasive imaging ...

  15. High Dynamic Range Imaging Using Multiple Exposures

    Science.gov (United States)

    Hou, Xinglin; Luo, Haibo; Zhou, Peipei; Zhou, Wei

    2017-06-01

    It is challenging to capture a high-dynamic range (HDR) scene using a low-dynamic range (LDR) camera. This paper presents an approach for improving the dynamic range of cameras by using multiple exposure images of same scene taken under different exposure times. First, the camera response function (CRF) is recovered by solving a high-order polynomial in which only the ratios of the exposures are used. Then, the HDR radiance image is reconstructed by weighted summation of the each radiance maps. After that, a novel local tone mapping (TM) operator is proposed for the display of the HDR radiance image. By solving the high-order polynomial, the CRF can be recovered quickly and easily. Taken the local image feature and characteristic of histogram statics into consideration, the proposed TM operator could preserve the local details efficiently. Experimental result demonstrates the effectiveness of our method. By comparison, the method outperforms other methods in terms of imaging quality.

  16. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  17. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    International Nuclear Information System (INIS)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver

    2015-01-01

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom

  18. Femtosecond photodissociation dynamics of I studied by ion imaging

    DEFF Research Database (Denmark)

    Larsen, J.J.; Bjerre, N.; Mørkbak, N.J.

    1998-01-01

    on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying...... agreement with quantum mechanical wave packet simulations. We discuss the perspectives for extending the studies to photochemical reactions of small polyatomic molecules...

  19. Thermal transpiration: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  20. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  1. How Dynamic Visualization Technology Can Support Molecular Reasoning

    Science.gov (United States)

    Levy, Dalit

    2013-01-01

    This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

  2. Molecular Imaging: A Useful Tool for the Development of Natural Killer Cell-Based Immunotherapies

    Directory of Open Access Journals (Sweden)

    Prakash Gangadaran

    2017-09-01

    Full Text Available Molecular imaging is a relatively new discipline that allows visualization, characterization, and measurement of the biological processes in living subjects, including humans, at a cellular and molecular level. The interaction between cancer cells and natural killer (NK cells is complex and incompletely understood. Despite our limited knowledge, progress in the search for immune cell therapies against cancer could be significantly improved by dynamic and non-invasive visualization and tracking of immune cells and by visualization of the response of cancer cells to therapies in preclinical and clinical studies. Molecular imaging is an essential tool for these studies, and a multimodal molecular imaging approach can be applied to monitor immune cells in vivo, for instance, to visualize therapeutic effects. In this review, we discuss the usefulness of NK cells in cancer therapies and the preclinical and clinical usefulness of molecular imaging in NK cell-based therapies. Furthermore, we discuss different molecular imaging modalities for use with NK cell-based therapies, and their preclinical and clinical applications in animal and human subjects. Molecular imaging has contributed to the development of NK cell-based therapies against cancers in animal models and to the refinement of current cell-based cancer immunotherapies. Developing sensitive and reproducible non-invasive molecular imaging technologies for in vivo NK cell monitoring and for real-time assessment of therapeutic effects will accelerate the development of NK cell therapies.

  3. Molecular beam studies of adsorption dynamics

    International Nuclear Information System (INIS)

    Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.

    1991-01-01

    We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential

  4. The research progress of nuclear medicine on cardiovascular molecular imaging

    International Nuclear Information System (INIS)

    Yin Xiaohua; Zhang Yongxue

    2007-01-01

    Cardiovascular molecular imaging is a rapidly evolving discipline and its clinical application is promising. Nuclear medicine is playing a leading role in this field with its special superiority of noninvasive, quantifiability, high sensitivity and specificity. It provides broad opportunities for exploring the pathophysiologic process of cardiovascular diseases and monitoring its gene therapy in the molecular level. In this review, we mainly discuss some basic knowledge on cardiovascular molecular imaging, and then focus on the applied research prospect of nuclear medicine radionuclide imaging. (authors)

  5. Multiparametric and molecular imaging of breast tumors with MRI and PET/MRI

    International Nuclear Information System (INIS)

    Pinker, K.; Marino, M.A.; Meyer-Baese, A.; Helbich, T.H.

    2016-01-01

    Magnetic resonance imaging (MRI) of the breast is an indispensable tool in breast imaging for many indications. Several functional parameters with MRI and positron emission tomography (PET) have been assessed for imaging of breast tumors and their combined application is defined as multiparametric imaging. Available data suggest that multiparametric imaging using different functional MRI and PET parameters can provide detailed information about the hallmarks of cancer and may provide additional specificity. Multiparametric and molecular imaging of the breast comprises established MRI parameters, such as dynamic contrast-enhanced MRI, diffusion-weighted imaging (DWI), MR proton spectroscopy ( 1 H-MRSI) as well as combinations of radiological and MRI techniques (e.g. PET/CT and PET/MRI) using radiotracers, such as fluorodeoxyglucose (FDG). Multiparametric and molecular imaging of the breast can be performed at different field-strengths (range 1.5-7 T). Emerging parameters comprise novel promising techniques, such as sodium imaging ( 23 Na MRI), phosphorus spectroscopy ( 31 P-MRSI), chemical exchange saturation transfer (CEST) imaging, blood oxygen level-dependent (BOLD) and hyperpolarized MRI as well as various specific radiotracers. Multiparametric and molecular imaging has multiple applications in breast imaging. Multiparametric and molecular imaging of the breast is an evolving field that will enable improved detection, characterization, staging and monitoring for personalized medicine in breast cancer. (orig.) [de

  6. Molecular ultrasound imaging: current status and future directions

    International Nuclear Information System (INIS)

    Deshpande, N.; Needles, A.; Willmann, J.K.

    2010-01-01

    Targeted contrast-enhanced ultrasound (molecular ultrasound) is an emerging imaging strategy that combines ultrasound technology with novel molecularly-targeted ultrasound contrast agents for assessing biological processes at the molecular level. Molecular ultrasound contrast agents are nano- or micro-sized particles that are targeted to specific molecular markers by adding high-affinity binding ligands onto the surface of the particles. Following intravenous administration, these targeted ultrasound contrast agents accumulate at tissue sites overexpressing specific molecular markers, thereby enhancing the ultrasound imaging signal. High spatial and temporal resolution, real-time imaging, non-invasiveness, relatively low costs, lack of ionising irradiation and wide availability of ultrasound systems are advantages compared to other molecular imaging modalities. In this article we review current concepts and future directions of molecular ultrasound imaging, including different classes of molecular ultrasound contrast agents, ongoing technical developments of pre-clinical and clinical ultrasound systems, the potential of molecular ultrasound for imaging different diseases at the molecular level, and the translation of molecular ultrasound into the clinic.

  7. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  8. Molecular dynamics studies of displacement cascades

    International Nuclear Information System (INIS)

    Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.

    1990-02-01

    Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs

  9. A molecular dynamics simulation code ISIS

    International Nuclear Information System (INIS)

    Kambayashi, Shaw

    1992-06-01

    Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)

  10. Spin-diffusions and diffusive molecular dynamics

    Science.gov (United States)

    Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

    2017-12-01

    Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

  11. Molecular imaging in the era of personalized medicine.

    Science.gov (United States)

    Jung, Kyung-Ho; Lee, Kyung-Han

    2015-01-01

    Clinical imaging creates visual representations of the body interior for disease assessment. The role of clinical imaging significantly overlaps with that of pathology, and diagnostic workflows largely depend on both fields. The field of clinical imaging is presently undergoing a radical change through the emergence of a new field called molecular imaging. This new technology, which lies at the intersection between imaging and molecular biology, enables noninvasive visualization of biochemical processes at the molecular level within living bodies. Molecular imaging differs from traditional anatomical imaging in that biomarkers known as imaging probes are used to visualize target molecules-of-interest. This ability opens up exciting new possibilities for applications in oncologic, neurological and cardiovascular diseases. Molecular imaging is expected to make major contributions to personalized medicine by allowing earlier diagnosis and predicting treatment response. The technique is also making a huge impact on pharmaceutical development by optimizing preclinical and clinical tests for new drug candidates. This review will describe the basic principles of molecular imaging and will briefly touch on three examples (from an immense list of new techniques) that may contribute to personalized medicine: receptor imaging, angiogenesis imaging, and apoptosis imaging.

  12. Dynamic imaging of oropharyngeal swallowing

    International Nuclear Information System (INIS)

    Fanucci, A.; Cerro, P.; Diotallevi, P.; Metastasio, F.; Fanucci, E.

    1991-01-01

    Oropharyngeal swallowing is too fast and complex a motion for the human eye to seize its various phases and subsequently evaluate morphology and function of the anatomical structures involved. A chronological subdivision of the swallowing act is needed for e step-by-step analysis. Dinamic evaluation of oropharyngeal swallowing by means of fluoroscopic and US videorecording proved to be a reliable method. Echovideorecording allowed tongue movements to be depicted, together with bolus formation and propulsion. Fluorovideorecording (U-Matic Sony unit, 25-30 images/sec) demonstrated pharyngeal and esophageal phases. A series of chronological and morphological reference points, which characterize oropharyngeal swallowing, were employed to analyze videorecorded images. Slowmotion mode, 'freezed' images, and rewinding allowed an easy and accurate evaluation of swallowing details. Combined chronological and morphological pieces of information allow a comprehensive evaluation of the swallowing act

  13. Molecular dynamics simulation of gold cluster growth during sputter deposition

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)

    2016-05-14

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  14. Magnetic resonance imaging of vulnerable atherosclerotic plaques: current imaging strategies and molecular imaging probes

    NARCIS (Netherlands)

    Briley-Saebo, Karen C.; Mulder, Willem J. M.; Mani, Venkatesh; Hyafil, Fabien; Amirbekian, Vardan; Aguinaldo, Juan Gilberto S.; Fisher, Edward A.; Fayad, Zahi A.

    2007-01-01

    The vulnerability or destabilization of atherosclerotic plaques has been directly linked to plaque composition. Imaging modalities, such as magnetic resonance (MR) imaging, that allow for evaluation of plaque composition at a cellular and molecular level, could further improve the detection of

  15. Translational research of optical molecular imaging for personalized medicine.

    Science.gov (United States)

    Qin, C; Ma, X; Tian, J

    2013-12-01

    In the medical imaging field, molecular imaging is a rapidly developing discipline and forms many imaging modalities, providing us effective tools to visualize, characterize, and measure molecular and cellular mechanisms in complex biological processes of living organisms, which can deepen our understanding of biology and accelerate preclinical research including cancer study and medicine discovery. Among many molecular imaging modalities, although the penetration depth of optical imaging and the approved optical probes used for clinics are limited, it has evolved considerably and has seen spectacular advances in basic biomedical research and new drug development. With the completion of human genome sequencing and the emergence of personalized medicine, the specific drug should be matched to not only the right disease but also to the right person, and optical molecular imaging should serve as a strong adjunct to develop personalized medicine by finding the optimal drug based on an individual's proteome and genome. In this process, the computational methodology and imaging system as well as the biomedical application regarding optical molecular imaging will play a crucial role. This review will focus on recent typical translational studies of optical molecular imaging for personalized medicine followed by a concise introduction. Finally, the current challenges and the future development of optical molecular imaging are given according to the understanding of the authors, and the review is then concluded.

  16. Modeling shockwave deformation via molecular dynamics

    International Nuclear Information System (INIS)

    Holian, B.L.

    1987-01-01

    Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too

  17. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  18. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  19. Molecular Imaging and Therapy of Merkel Cell Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Beylergil, Volkan, E-mail: beylergv@mskcc.org [Molecular and Imaging Therapy Service, Department of Radiology Box 77, Memorial Sloan-Kettering Cancer Center 1275 York Ave, New York, NY 10065 (United States); Carrasquillo, Jorge A. [Molecular and Imaging Therapy Service, Department of Radiology Box 77, Memorial Sloan-Kettering Cancer Center 1275 York Ave, New York, NY 10065 (United States); Department of Radiology, Weill Cornell Medical Center, New York, NY 10065 (United States)

    2014-04-29

    Several molecular imaging modalities have been evaluated in the management of Merkel cell carcinoma (MCC), a rare and aggressive tumor with a high tendency to metastasize. Continuous progress in the field of molecular imaging might improve management in these patients. The authors review the current modalities and their impact on MCC in this brief review article.

  20. Molecular Imaging and Therapy of Merkel Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Volkan Beylergil

    2014-04-01

    Full Text Available Several molecular imaging modalities have been evaluated in the management of Merkel cell carcinoma (MCC, a rare and aggressive tumor with a high tendency to metastasize. Continuous progress in the field of molecular imaging might improve management in these patients. The authors review the current modalities and their impact on MCC in this brief review article.

  1. Molecular Imaging and Precision Medicine in Prostate Cancer.

    Science.gov (United States)

    Ceci, Francesco; Fiorentino, Michelangelo; Castellucci, Paolo; Fanti, Stefano

    2017-01-01

    The aim of the present review is to discuss about the role of new probes for molecular imaging in the evaluation of prostate cancer (PCa). This review focuses particularly on the role of new promising radiotracers for the molecular imaging with PET/computed tomography in the detection of PCa recurrence. The role of these new imaging techniques to guide lesion-target therapies and the potential application of these molecular probes as theranostics agents is discussed. Finally, the molecular mechanisms underlying resistance to castration in PCa and the maintenance of active androgen receptor are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Understanding synthesis imaging dynamic range

    Science.gov (United States)

    Braun, R.

    2013-03-01

    We develop a general framework for quantifying the many different contributions to the noise budget of an image made with an array of dishes or aperture array stations. Each noise contribution to the visibility data is associated with a relevant correlation timescale and frequency bandwidth so that the net impact on a complete observation can be assessed when a particular effect is not captured in the instrumental calibration. All quantities are parameterised as function of observing frequency and the visibility baseline length. We apply the resulting noise budget analysis to a wide range of existing and planned telescope systems that will operate between about 100 MHz and 5 GHz to ascertain the magnitude of the calibration challenges that they must overcome to achieve thermal noise limited performance. We conclude that calibration challenges are increased in several respects by small dimensions of the dishes or aperture array stations. It will be more challenging to achieve thermal noise limited performance using 15 m class dishes rather than the 25 m dishes of current arrays. Some of the performance risks are mitigated by the deployment of phased array feeds and more with the choice of an (alt,az,pol) mount, although a larger dish diameter offers the best prospects for risk mitigation. Many improvements to imaging performance can be anticipated at the expense of greater complexity in calibration algorithms. However, a fundamental limitation is ultimately imposed by an insufficient number of data constraints relative to calibration variables. The upcoming aperture array systems will be operating in a regime that has never previously been addressed, where a wide range of effects are expected to exceed the thermal noise by two to three orders of magnitude. Achieving routine thermal noise limited imaging performance with these systems presents an extreme challenge. The magnitude of that challenge is inversely related to the aperture array station diameter.

  3. Molecular dynamics using quasielastic neutron scattering

    CERN Document Server

    Mitra, S

    2003-01-01

    Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)

  4. Dynamic metamaterial aperture for microwave imaging

    International Nuclear Information System (INIS)

    Sleasman, Timothy; Imani, Mohammadreza F.; Gollub, Jonah N.; Smith, David R.

    2015-01-01

    We present a dynamic metamaterial aperture for use in computational imaging schemes at microwave frequencies. The aperture consists of an array of complementary, resonant metamaterial elements patterned into the upper conductor of a microstrip line. Each metamaterial element contains two diodes connected to an external control circuit such that the resonance of the metamaterial element can be damped by application of a bias voltage. Through applying different voltages to the control circuit, select subsets of the elements can be switched on to create unique radiation patterns that illuminate the scene. Spatial information of an imaging domain can thus be encoded onto this set of radiation patterns, or measurements, which can be processed to reconstruct the targets in the scene using compressive sensing algorithms. We discuss the design and operation of a metamaterial imaging system and demonstrate reconstructed images with a 10:1 compression ratio. Dynamic metamaterial apertures can potentially be of benefit in microwave or millimeter wave systems such as those used in security screening and through-wall imaging. In addition, feature-specific or adaptive imaging can be facilitated through the use of the dynamic aperture

  5. Dynamic metamaterial aperture for microwave imaging

    Energy Technology Data Exchange (ETDEWEB)

    Sleasman, Timothy; Imani, Mohammadreza F.; Gollub, Jonah N.; Smith, David R. [Center for Metamaterials and Integrated Plasmonics, Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, 27708 (United States)

    2015-11-16

    We present a dynamic metamaterial aperture for use in computational imaging schemes at microwave frequencies. The aperture consists of an array of complementary, resonant metamaterial elements patterned into the upper conductor of a microstrip line. Each metamaterial element contains two diodes connected to an external control circuit such that the resonance of the metamaterial element can be damped by application of a bias voltage. Through applying different voltages to the control circuit, select subsets of the elements can be switched on to create unique radiation patterns that illuminate the scene. Spatial information of an imaging domain can thus be encoded onto this set of radiation patterns, or measurements, which can be processed to reconstruct the targets in the scene using compressive sensing algorithms. We discuss the design and operation of a metamaterial imaging system and demonstrate reconstructed images with a 10:1 compression ratio. Dynamic metamaterial apertures can potentially be of benefit in microwave or millimeter wave systems such as those used in security screening and through-wall imaging. In addition, feature-specific or adaptive imaging can be facilitated through the use of the dynamic aperture.

  6. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  7. Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

    National Research Council Canada - National Science Library

    Johnston, K

    1998-01-01

    .... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

  8. Molecular Dynamics and Bioactivity of a Novel Mutated Human ...

    African Journals Online (AJOL)

    Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...

  9. Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting

    National Research Council Canada - National Science Library

    Low, Tammy K

    2006-01-01

    .... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...

  10. A molecular dynamics calculation of solid phase of malonic acid ...

    Indian Academy of Sciences (India)

    Sathya S R R Perumal

    Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...

  11. Gd-DTPA-enhanced dynamic MR imaging

    International Nuclear Information System (INIS)

    Frank, J.A.; Choyke, P.L.; Carvlin, M.; Inscoe, S.; Austin, H.; Dwyer, A.J.; Girton, M.; Black, J.

    1988-01-01

    This paper describes dynamic enhanced renal MR imaging, a new method of identifying specific derangements in renal function. Various diuretics were employed in 45 animal experiments to demonstrate the effects on the normal renal enhancement pattern (EP) after Gd-DTPA. Since different diuretics, osmotic (O), carbonic anhydrase (CA), and loop (L), are active at different sites, specific EP alterations are observed. Imaging was performed with 32 5.1-second sequential gradient recalled acquisition in a steady state images following a bolus of Gd-DTPA

  12. Molecular dynamics and Monte Carlo calculations in statistical mechanics

    International Nuclear Information System (INIS)

    Wood, W.W.; Erpenbeck, J.J.

    1976-01-01

    Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

  13. Next generation extended Lagrangian first principles molecular dynamics.

    Science.gov (United States)

    Niklasson, Anders M N

    2017-08-07

    Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

  14. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  15. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  16. Women's preferences of dynamic spectral imaging colposcopy

    NARCIS (Netherlands)

    Louwers, J.A.; Zaal, Afra; Kocken, M.; Papagiannakis, E.; Meijer, C.J.; Verheijen, RHM

    2015-01-01

    Background: The focus of testing the dynamic spectral imaging (DSI) colposcope has been on the technical characteristics and clinical performance. However, aspects from a patient’s perspective are just as important. Methods: This study was designed as a substudy of the DSI validation study, a

  17. A fermionic molecular dynamics technique to model nuclear matter

    International Nuclear Information System (INIS)

    Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

    2009-01-01

    Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

  18. Current-driven dynamics in molecular-scale devices

    International Nuclear Information System (INIS)

    Seideman, Tamar

    2003-01-01

    We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

  19. Dynamic high resolution imaging of rats

    International Nuclear Information System (INIS)

    Miyaoka, R.S.; Lewellen, T.K.; Bice, A.N.

    1990-01-01

    A positron emission tomography with the sensitivity and resolution to do dynamic imaging of rats would be an invaluable tool for biological researchers. In this paper, the authors determine the biological criteria for dynamic positron emission imaging of rats. To be useful, 3 mm isotropic resolution and 2-3 second time binning were necessary characteristics for such a dedicated tomograph. A single plane in which two objects of interest could be imaged simultaneously was considered acceptable. Multi-layered detector designs were evaluated as a possible solution to the dynamic imaging and high resolution imaging requirements. The University of Washington photon history generator was used to generate data to investigate a tomograph's sensitivity to true, scattered and random coincidences for varying detector ring diameters. Intrinsic spatial uniformity advantages of multi-layered detector designs over conventional detector designs were investigated using a Monte Carlo program. As a result, a modular three layered detector prototype is being developed. A module will consist of a layer of five 3.5 mm wide crystals and two layers of six 2.5 mm wide crystals. The authors believe adequate sampling can be achieved with a stationary detector system using these modules. Economical crystal decoding strategies have been investigated and simulations have been run to investigate optimum light channeling methods for block decoding strategies. An analog block decoding method has been proposed and will be experimentally evaluated to determine whether it can provide the desired performance

  20. Molecular Dynamic Modeling and Simulation for Polymers

    National Research Council Canada - National Science Library

    Harrell, Anthony

    2003-01-01

    ... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...

  1. Molecular dynamics of a proguanil derivative

    African Journals Online (AJOL)

    pc

    Proguanil is a prophylactic antimalarial drug t .... presence of resistance to individual component. ... This is the mathematical ... predicting equilibrium structures of molecular systems ..... for the modeling and subsequent development of.

  2. Resonance Energy Transfer Molecular Imaging Application in Biomedicine

    Directory of Open Access Journals (Sweden)

    NIE Da-hong1,2;TANG Gang-hua1,3

    2016-11-01

    Full Text Available Resonance energy transfer molecular imaging (RETI can markedly improve signal intensity and tissue penetrating capacity of optical imaging, and have huge potential application in the deep-tissue optical imaging in vivo. Resonance energy transfer (RET is an energy transition from the donor to an acceptor that is in close proximity, including non-radiative resonance energy transfer and radiative resonance energy transfer. RETI is an optical imaging technology that is based on RET. RETI mainly contains fluorescence resonance energy transfer imaging (FRETI, bioluminescence resonance energy transfer imaging (BRETI, chemiluminescence resonance energy transfer imaging (CRETI, and radiative resonance energy transfer imaging (RRETI. RETI is the hot field of molecular imaging research and has been widely used in the fields of biology and medicine. This review mainly focuses on RETI principle and application in biomedicine.

  3. Computational methods in molecular imaging technologies

    CERN Document Server

    Gunjan, Vinit Kumar; Venkatesh, C; Amarnath, M

    2017-01-01

    This book highlights the experimental investigations that have been carried out on magnetic resonance imaging and computed tomography (MRI & CT) images using state-of-the-art Computational Image processing techniques, and tabulates the statistical values wherever necessary. In a very simple and straightforward way, it explains how image processing methods are used to improve the quality of medical images and facilitate analysis. It offers a valuable resource for researchers, engineers, medical doctors and bioinformatics experts alike.

  4. Visualizing functional motions of membrane transporters with molecular dynamics simulations.

    Science.gov (United States)

    Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

    2013-01-29

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

  5. Dynamic MR imaging of the sellar region

    International Nuclear Information System (INIS)

    Takahashi, M.; Sakamoto, Y.; Korogi, Y.; Nishimura, R.; Yoshizumi, K.; Ushio, Y.

    1990-01-01

    This paper reports on sequential and differential enhancement of the normal and abnormal structures of the sellar regions were evaluated with dynamic MR imaging for the diagnosis of sellar and parasellar tumors. Dynamic MR imaging was performed on a 1.5-T superconductive unit, with rapid injection of Gd-DTPA (0.1 mmol/kg body weight) followed by serial spin-echo (TR 220/TE 15 msec) images of the sellar region for 3-5 minutes. The first structures visualized were the cavernous sinus, infundibulum, and posterior pituitary lobe within 30 seconds, followed by enhancement of the anterior pituitary lobe near the infundibulum in 50 seconds and the peripheral portion of the anterior pituitary lobe in 80 seconds

  6. Pseudorotational dynamics of small molecular species

    International Nuclear Information System (INIS)

    Hagelberg, F.

    2002-01-01

    The electron nuclear dynamics (END) theory was designed to provide a full description of the dynamic development of the electronic system. It is independent of any potential energy surface constructions. The dynamic behavior of molecules close to the threshold of dissociation was the objective of this study. Thus, simulations based on END theory were performed with the aim to extend the current understanding of the dynamic features of pseudorotational into a non-adiabatic regime. Electron dynamics of triatomic species (H 3 + and Li 3 + ) in terms of electronic angular momentum expectation values were characterized. Finally, it is shown that the expansion coefficients which carry the information about the excitation content of the electronic system at any stage of the motional process can be calculated. (nevyjel)

  7. The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

    Science.gov (United States)

    Chen, Jundong

    2018-03-01

    Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

  8. Imaging Electron Dynamics with Ultrashort Light Pulses: A Theory Perspective

    Directory of Open Access Journals (Sweden)

    Daria Popova-Gorelova

    2018-02-01

    Full Text Available A wide range of ultrafast phenomena in various atomic, molecular and condense matter systems is governed by electron dynamics. Therefore, the ability to image electronic motion in real space and real time would provide a deeper understanding of such processes and guide developments of tools to control them. Ultrashort light pulses, which can provide unprecedented time resolution approaching subfemtosecond time scale, are perspective to achieve real-time imaging of electron dynamics. This task is challenging not only from an experimental view, but also from a theory perspective, since standard theories describing light-matter interaction in a stationary regime can provide erroneous results in an ultrafast case as demonstrated by several theoretical studies. We review the theoretical framework based on quantum electrodynamics, which has been shown to be necessary for an accurate description of time-resolved imaging of electron dynamics with ultrashort light pulses. We compare the results of theoretical studies of time-resolved nonresonant and resonant X-ray scattering, and time- and angle-resolved photoelectron spectroscopy and show that the corresponding time-resolved signals encode analogous information about electron dynamics. Thereby, the information about an electronic system provided by these time-resolved techniques is different from the information provided by their time-independent analogues.

  9. Molecular imaging in the framework of personalized cancer medicine.

    Science.gov (United States)

    Belkić, Dzevad; Belkić, Karen

    2013-11-01

    With our increased understanding of cancer cell biology, molecular imaging offers a strategic bridge to oncology. This complements anatomic imaging, particularly magnetic resonance (MR) imaging, which is sensitive but not specific. Among the potential harms of false positive findings is lowered adherence to recommended surveillance post-therapy and by persons at increased cancer risk. Positron emission tomography (PET) plus computerized tomography (CT) is the molecular imaging modality most widely used in oncology. In up to 40% of cases, PET-CT leads to changes in therapeutic management. Newer PET tracers can detect tumor hypoxia, bone metastases in androgen-sensitive prostate cancer, and human epidermal growth factor receptor type 2 (HER2)-expressive tumors. Magnetic resonance spectroscopy provides insight into several metabolites at the same time. Combined with MRI, this yields magnetic resonance spectroscopic imaging (MRSI), which does not entail ionizing radiation and is thus suitable for repeated monitoring. Using advanced signal processing, quantitative information can be gleaned about molecular markers of brain, breast, prostate and other cancers. Radiation oncology has benefited from molecular imaging via PET-CT and MRSI. Advanced mathematical approaches can improve dose planning in stereotactic radiosurgery, stereotactic body radiotherapy and high dose-rate brachytherapy. Molecular imaging will likely impact profoundly on clinical decision making in oncology. Molecular imaging via MR could facilitate early detection especially in persons at high risk for specific cancers.

  10. Dynamic Image Stitching for Panoramic Video

    Directory of Open Access Journals (Sweden)

    Jen-Yu Shieh

    2014-10-01

    Full Text Available The design of this paper is based on the Dynamic image titching for panoramic video. By utilizing OpenCV visual function data library and SIFT algorithm as the basis for presentation, this article brings forward Gaussian second differenced MoG which is processed basing on DoG Gaussian Difference Map to reduce order in synthesizing dynamic images and simplify the algorithm of the Gaussian pyramid structure. MSIFT matches with overlapping segmentation method to simplify the scope of feature extraction in order to enhance speed. And through this method traditional image synthesis can be improved without having to take lots of time in calculation and being limited by space and angle. This research uses four normal Webcams and two IPCAM coupled with several-wide angle lenses. By using wide-angle lenses to monitor over a wide range of an area and then by using image stitching panoramic effect is achieved. In terms of overall image application and control interface, Microsoft Visual Studio C# is adopted to a construct software interface. On a personal computer with 2.4-GHz CPU and 2-GB RAM and with the cameras fixed to it, the execution speed is three images per second, which reduces calculation time of the traditional algorithm.

  11. Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

    NARCIS (Netherlands)

    Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

    2007-01-01

    This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

  12. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  13. Luminescence imaging using radionuclides: a potential application in molecular imaging

    International Nuclear Information System (INIS)

    Park, Jeong Chan; Il An, Gwang; Park, Se-Il; Oh, Jungmin; Kim, Hong Joo; Su Ha, Yeong; Wang, Eun Kyung; Min Kim, Kyeong; Kim, Jung Young; Lee, Jaetae; Welch, Michael J.; Yoo, Jeongsoo

    2011-01-01

    Introduction: Nuclear and optical imaging are complementary in many aspects and there would be many advantages when optical imaging probes are prepared using radionuclides rather than classic fluorophores, and when nuclear and optical dual images are obtained using single imaging probe. Methods: The luminescence intensities of various radionuclides having different decay modes have been assayed using luminescence imaging and in vitro luminometer. Radioiodinated Herceptin was injected into a tumor-bearing mouse, and luminescence and microPET images were obtained. The plant dipped in [ 32 P]phosphate solution was scanned in luminescence mode. Radio-TLC plate was also imaged in the same imaging mode. Results: Radionuclides emitting high energy β + /β - particles showed higher luminescence signals. NIH3T6.7 tumors were detected in both optical and nuclear imaging. The uptake of [ 32 P]phosphate in plant was easily followed by luminescence imaging. Radio-TLC plate was visualized and radiochemical purity was quantified using luminescence imaging. Conclusion: Many radionuclides with high energetic β + or β - particles during decay were found to be imaged in luminescence mode due mainly to Cerenkov radiation. 'Cerenkov imaging' provides a new optical imaging platform and an invaluable bridge between optical and nuclear imaging. New optical imaging probes could be easily prepared using well-established radioiodination methods. Cerenkov imaging will have more applications in the research field of plant science and autoradiography.

  14. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  15. Ab initio molecular dynamics in a finite homogeneous electric field.

    Science.gov (United States)

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

  16. Classical and quantum molecular dynamics in NMR spectra

    CERN Document Server

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  17. Molecular dynamics with deterministic and stochastic numerical methods

    CERN Document Server

    Leimkuhler, Ben

    2015-01-01

    This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

  18. Image fusion for dynamic contrast enhanced magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Leach Martin O

    2004-10-01

    Full Text Available Abstract Background Multivariate imaging techniques such as dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI have been shown to provide valuable information for medical diagnosis. Even though these techniques provide new information, integrating and evaluating the much wider range of information is a challenging task for the human observer. This task may be assisted with the use of image fusion algorithms. Methods In this paper, image fusion based on Kernel Principal Component Analysis (KPCA is proposed for the first time. It is demonstrated that a priori knowledge about the data domain can be easily incorporated into the parametrisation of the KPCA, leading to task-oriented visualisations of the multivariate data. The results of the fusion process are compared with those of the well-known and established standard linear Principal Component Analysis (PCA by means of temporal sequences of 3D MRI volumes from six patients who took part in a breast cancer screening study. Results The PCA and KPCA algorithms are able to integrate information from a sequence of MRI volumes into informative gray value or colour images. By incorporating a priori knowledge, the fusion process can be automated and optimised in order to visualise suspicious lesions with high contrast to normal tissue. Conclusion Our machine learning based image fusion approach maps the full signal space of a temporal DCE-MRI sequence to a single meaningful visualisation with good tissue/lesion contrast and thus supports the radiologist during manual image evaluation.

  19. Translational Applications of Molecular Imaging and Radionuclide Therapy

    International Nuclear Information System (INIS)

    Welch, Michael J.; Eckelman, William C.; Vera, David

    2005-01-01

    Molecular imaging is becoming a larger part of imaging research and practice. The Office of Biological and Environmental Research of the Department of Energy funds a significant number of researchers in this area. The proposal is to partially fund a workshop to inform scientists working in nuclear medicine and nuclear medicine practitioners of the recent advances of molecular imaging in nuclear medicine as well as other imaging modalities. A limited number of topics related to radionuclide therapy will also be discussed. The proposal is to request partial funds for the workshop entitled ''Translational Applications of Molecular Imaging and Radionuclide Therapy'' to be held prior to the Society of Nuclear Medicine Annual Meeting in Toronto, Canada in June 2005. The meeting will be held on June 17-18. This will allow scientists interested in all aspects of nuclear medicine imaging to attend. The chair of the organizing group is Dr. Michael J. Welch. The organizing committee consists of Dr. Welch, Dr. William C. Eckelman and Dr. David Vera. The goal is to invite speakers to discuss the most recent advances of modern molecular imaging and therapy. Speakers will present advances made in in vivo tagging imaging assays, technical aspects of small animal imaging, in vivo imaging and bench to bedside translational study; and the role of a diagnostic scan on therapy selection. This latter topic will include discussions on therapy and new approaches to dosimetry. Several of these topics are those funded by the Department of Energy Office of Biological and Environmental Research

  20. Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Chengzhen Sun; Bofeng Bai

    2017-01-01

    Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

  1. First principles molecular dynamics without self-consistent field optimization

    International Nuclear Information System (INIS)

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-01

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

  2. High dynamic range imaging sensors and architectures

    CERN Document Server

    Darmont, Arnaud

    2013-01-01

    Illumination is a crucial element in many applications, matching the luminance of the scene with the operational range of a camera. When luminance cannot be adequately controlled, a high dynamic range (HDR) imaging system may be necessary. These systems are being increasingly used in automotive on-board systems, road traffic monitoring, and other industrial, security, and military applications. This book provides readers with an intermediate discussion of HDR image sensors and techniques for industrial and non-industrial applications. It describes various sensor and pixel architectures capable

  3. Molecular Imaging of Tumors Using a Quantitative T1 Mapping Technique via Magnetic Resonance Imaging

    Directory of Open Access Journals (Sweden)

    Kelsey Herrmann

    2015-07-01

    Full Text Available Magnetic resonance imaging (MRI of glioblastoma multiforme (GBM with molecular imaging agents would allow for the specific localization of brain tumors. Prior studies using T1-weighted MR imaging demonstrated that the SBK2-Tris-(Gd-DOTA3 molecular imaging agent labeled heterotopic xenograft models of brain tumors more intensely than non-specific contrast agents using conventional T1-weighted imaging techniques. In this study, we used a dynamic quantitative T1 mapping strategy to more objectively compare intra-tumoral retention of the SBK2-Tris-(Gd-DOTA3 agent over time in comparison to non-targeted control agents. Our results demonstrate that the targeted SBK2-Tris-(Gd-DOTA3 agent, a scrambled-Tris-(Gd-DOTA3 control agent, and the non-specific clinical contrast agent Optimark™ all enhanced flank tumors of human glioma cells with similar maximal changes on T1 mapping. However, the retention of the agents differs. The non-specific agents show significant recovery within 20 min by an increase in T1 while the specific agent SBK2-Tris-(Gd-DOTA3 is retained in the tumors and shows little recovery over 60 min. The retention effect is demonstrated by percent change in T1 values and slope calculations as well as by calculations of gadolinium concentration in tumor compared to muscle. Quantitative T1 mapping demonstrates the superior binding and retention in tumors of the SBK2-Tris-(Gd-DOTA3 agent over time compared to the non-specific contrast agent currently in clinical use.

  4. Cardiac fluid dynamics meets deformation imaging.

    Science.gov (United States)

    Dal Ferro, Matteo; Stolfo, Davide; De Paris, Valerio; Lesizza, Pierluigi; Korcova, Renata; Collia, Dario; Tonti, Giovanni; Sinagra, Gianfranco; Pedrizzetti, Gianni

    2018-02-20

    Cardiac function is about creating and sustaining blood in motion. This is achieved through a proper sequence of myocardial deformation whose final goal is that of creating flow. Deformation imaging provided valuable contributions to understanding cardiac mechanics; more recently, several studies evidenced the existence of an intimate relationship between cardiac function and intra-ventricular fluid dynamics. This paper summarizes the recent advances in cardiac flow evaluations, highlighting its relationship with heart wall mechanics assessed through the newest techniques of deformation imaging and finally providing an opinion of the most promising clinical perspectives of this emerging field. It will be shown how fluid dynamics can integrate volumetric and deformation assessments to provide a further level of knowledge of cardiac mechanics.

  5. Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

    Science.gov (United States)

    Negre, Christian

    2017-06-01

    A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

  6. Nanobody: The “Magic Bullet” for Molecular Imaging?

    Science.gov (United States)

    Chakravarty, Rubel; Goel, Shreya; Cai, Weibo

    2014-01-01

    Molecular imaging involves the non-invasive investigation of biological processes in vivo at the cellular and molecular level, which can play diverse roles in better understanding and treatment of various diseases. Recently, single domain antigen-binding fragments known as 'nanobodies' were bioengineered and tested for molecular imaging applications. Small molecular size (~15 kDa) and suitable configuration of the complementarity determining regions (CDRs) of nanobodies offer many desirable features suitable for imaging applications, such as rapid targeting and fast blood clearance, high solubility, high stability, easy cloning, modular nature, and the capability of binding to cavities and difficult-to-access antigens. Using nanobody-based probes, several imaging techniques such as radionuclide-based, optical and ultrasound have been employed for visualization of target expression in various disease models. This review summarizes the recent developments in the use of nanobody-based probes for molecular imaging applications. The preclinical data reported to date are quite promising, and it is expected that nanobody-based molecular imaging agents will play an important role in the diagnosis and management of various diseases. PMID:24578722

  7. MRI Reporter Genes for Noninvasive Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Caixia Yang

    2016-05-01

    Full Text Available Magnetic resonance imaging (MRI is one of the most important imaging technologies used in clinical diagnosis. Reporter genes for MRI can be applied to accurately track the delivery of cell in cell therapy, evaluate the therapy effect of gene delivery, and monitor tissue/cell-specific microenvironments. Commonly used reporter genes for MRI usually include genes encoding the enzyme (e.g., tyrosinase and β-galactosidase, the receptor on the cells (e.g., transferrin receptor, and endogenous reporter genes (e.g., ferritin reporter gene. However, low sensitivity limits the application of MRI and reporter gene-based multimodal imaging strategies are common including optical imaging and radionuclide imaging. These can significantly improve diagnostic efficiency and accelerate the development of new therapies.

  8. Incoherent imaging using dynamically scattered coherent electrons

    International Nuclear Information System (INIS)

    Nellist, P.D.; Pennycook, S.J.

    1999-01-01

    We use a Bloch wave approach to show that, even for coherent dynamical scattering from a stationary lattice with no absorption, annular dark-field imaging in a scanning transmission electron microscope gives a direct incoherent structure image of the atomic-column positions of a zone-axis-aligned crystal. Although many Bloch waves may be excited by the probe, the detector provides a filtering effect so that the 1s-type bound states are found to dominate the image contrast for typical experimental conditions. We also find that the column intensity is related to the transverse kinetic energy of the 1s states, which gives atomic number, Z, contrast. The additional effects of phonon scattering are discussed, in particular the reasons why phonon scattering is not a prerequisite for transverse incoherence. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  9. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Jeffrey [ORNL; Bilheux, Hassina Z [ORNL; Kang, Misun [ORNL; Voisin, Sophie [ORNL; Cheng, Chu-Lin [ORNL; Horita, Jusuke [ORNL; Perfect, Edmund [ORNL

    2013-01-01

    Many terrestrial ecosystem processes are constrained by water availability and transport within the soil. Knowledge of plant water fluxes is thus critical for assessing mechanistic processes linked to biogeochemical cycles, yet resolution of root structure and xylem water transport dynamics has been a particularly daunting task for the ecologist. Through neutron imaging, we demonstrate the ability to non-invasively monitor individual root functionality and water fluxes within Zea mays L. (maize) and Panicum virgatum L. (switchgrass) seedlings growing in a sandy medium. Root structure and growth were readily imaged by neutron radiography and neutron computed tomography. Seedlings were irrigated with water or deuterium oxide and imaged through time as a growth lamp was cycled on to alter leaf demand for water. Sub-millimeter scale resolution reveals timing and magnitudes of root water uptake, redistribution within the roots, and root-shoot hydraulic linkages, relationships not well characterized by other techniques.

  10. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

    Science.gov (United States)

    Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C

    2013-11-07

    Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

  11. Molecular imaging of cancer using PET and SPECT

    DEFF Research Database (Denmark)

    Kjaer, Andreas

    2006-01-01

    for molecular imaging of cancer. Especially the possibility of a quick transfer of methods developed in animals to patients (translational research) is an important strength. This article will briefly discuss the newest applications and their importance and perspective in relation to the shift in paradigm......Molecular imaging allows for the study of molecular and cellular events in the living intact organism. The nuclear medicine methodologies of positron emission tomography (PET) and single photon emission computer tomography (SPECT) posses several advantages, which make them particularly suited...

  12. Molecular Imaging and Precision Medicine in Dementia and Movement Disorders.

    Science.gov (United States)

    Mallik, Atul K; Drzezga, Alexander; Minoshima, Satoshi

    2017-01-01

    Precision medicine (PM) has been defined as "prevention and treatment strategies that take individual variability into account." Molecular imaging (MI) is an ideally suited tool for PM approaches to neurodegenerative dementia and movement disorders (MD). Here we review PM approaches and discuss how they may be applied to other associated neurodegenerative dementia and MD. With ongoing major therapeutic research initiatives that include the use of molecular imaging, we look forward to established interventions targeted to specific molecular pathophysiology and expect the potential benefit of MI PM approaches in neurodegenerative dementia and MD will only increase. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Molecular dynamics study of atomic displacements in disordered solid alloys

    Science.gov (United States)

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  14. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

  15. Nuclear Molecular Imaging Strategies in Immune Checkpoint Inhibitor Therapy

    DEFF Research Database (Denmark)

    Guldbrandsen, Kasper F; Hendel, Helle W; Langer, Seppo W

    2017-01-01

    this, new response criteria for evaluating these patients with morphologic imaging have been proposed. The aim of this paper is to review and discuss the current evidence for the use of molecular imaging, e.g., PET/CT (Positron Emission Tomography/Computer Tomography) with18F-Fluorodeoxyglucoes (FDG...

  16. Molecular mass spectrometry imaging in biomedical and life science research

    Czech Academy of Sciences Publication Activity Database

    Pól, Jaroslav; Strohalm, Martin; Havlíček, Vladimír; Volný, Michael

    2010-01-01

    Roč. 134, č. 5 (2010), s. 423-443 ISSN 0948-6143 R&D Projects: GA MŠk LC545; GA ČR GPP206/10/P018 Institutional research plan: CEZ:AV0Z50200510 Keywords : Mass spectrometry * Chemical imaging * Molecular imaging Subject RIV: EE - Microbiology, Virology Impact factor: 4.727, year: 2010

  17. Dynamic molecular oxygen production in cometary comae

    Science.gov (United States)

    Yao, Yunxi; Giapis, Konstantinos P.

    2017-05-01

    Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.

  18. Novel approach to improve molecular imaging research: Correlation between macroscopic and molecular pathological findings in patients

    Energy Technology Data Exchange (ETDEWEB)

    Boehm, Ingrid, E-mail: i.boehm@uni-bonn.de [Department of Diagnostic Radiology, ZARF Project, Center for Molecular Imaging Research MBMB, Philipps University of Marburg, Baldingerstrasse, 35039 Marburg (Germany)

    2011-09-15

    Purpose: Currently, clinical research approaches are sparse in molecular imaging studies. Moreover, possible links between imaging features and pathological laboratory parameters are unknown, so far. Therefore, the goal was to find a possible relationship between imaging features and peripheral blood cell apoptosis, and thereby to present a novel way to complement molecular imaging research. Materials and methods: The investigation has been done in systemic lupus erythematosus (SLE), a prototype of an autoimmune disease characterized by multiorgan involvement, autoantibody production, and disturbed apoptosis. Retrospectively, radiological findings have been compared to both autoantibody findings and percentage apoptotic blood cells. Results: Two SLE groups could be identified: patients with normal (annexin V binding < 20%), and with increased apoptosis (annexin V binding > 20%) of peripheral blood cells. The frequency of radiological examinations in SLE patients significantly correlated with an increased percentage of apoptotic cells (p < 0.005). In patients with characteristic imaging findings (e.g. lymph node swelling, pleural effusion) an elevated percentage of apoptotic cells was present. In contrast SLE-patients with normal imaging findings or uncharacteristic results of minimal severity had normal percentages of apoptotic blood cells. Conclusion: This correlation between radiographic findings and percentage of apoptotic blood cells provides (1) further insight into pathological mechanisms of SLE, (2) will offer the possibility to introduce apoptotic biomarkers as molecular probes for clinical molecular imaging approaches in future to early diagnose organ complaints in patients with SLE, and (3) is a plea to complement molecular imaging research by this clinical approach.

  19. The development of nanobody probes for molecular imaging

    International Nuclear Information System (INIS)

    Ding Zhiling; Lan Xiaoli; Zhang Yongxue

    2014-01-01

    The nanobody is a novel antibody fragment, which has beneficial biophysical and pharmacokinetic properties, such as the small molecular weight, high affinity and specificity for antigen. Nanobody is ideally suitable for molecular imaging as a targeting probe that could label antigen at nmol level in vitro. In animal models of xenografted tumor, atherosclerotic plaques and brain disorders, the target tissues were specifically and clearly detected and the high tumor-to-blood (T/B) ratios were obtained. Structural or chemical modified nanobodies will have higher affinity and retention to target tissues, and be convenient for the application of molecular imaging. With the development of the related research, nanobody-based molecular imaging will be gradually transformed into the clinical applications, and play an important role in early diagnosis and therapeutic assessment. (authors)

  20. Dynamics of Corticosteroid Receptors: Lessons from Live Cell Imaging

    International Nuclear Information System (INIS)

    Nishi, Mayumi

    2011-01-01

    Adrenal corticosteroids (cortisol in humans or corticosterone in rodents) exert numerous effects on the central nervous system that regulates the stress response, mood, learning and memory, and various neuroendocrine functions. Corticosterone (CORT) actions in the brain are mediated via two receptor systems: the glucocorticoid receptor (GR) and the mineralocorticoid receptor (MR). It has been shown that GR and MR are highly colocalized in the hippocampus. These receptors are mainly distributed in the cytoplasm without hormones and translocated into the nucleus after treatment with hormones to act as transcriptional factors. Thus the subcellular dynamics of both receptors are one of the most important issues. Given the differential action of MR and GR in the central nervous system, it is of great consequence to clarify how these receptors are trafficked between cytoplasm and nucleus and their interactions are regulated by hormones and/or other molecules to exert their transcriptional activity. In this review, we focus on the nucleocytoplasmic and subnuclear trafficking of GR and MR in neural cells and non-neural cells analyzed by using molecular imaging techniques with green fluorescent protein (GFP) including fluorescence recovery after photobleaching (FRAP) and fluorescence resonance energy transfer (FRET), and discuss various factors affecting the dynamics of these receptors. Furthermore, we discuss the future directions of in vivo molecular imaging of corticosteroid receptors at the whole brain level

  1. Mechanically magnified imaging of molecular interferograms

    International Nuclear Information System (INIS)

    Stibor, A.; Stefanov, A.; Goldfarb, F.; Reiger, E.; Arndt, M.

    2005-01-01

    Full text: Imaging of surface adsorbed molecules is presented as a valuable detection method for matter interferometry with fluorescent particles. A mechanical magnification scheme is implemented to circumvent the optical resolution limit. Mechanically magnified fluorescence imaging turns out to be an excellent tool for recording quantum interference patterns with high visibility. A unique advantage of this technique is its scalability: for certain classes of nanosized objects, the detection sensitivity will even increase significantly with increasing size of the particle. (author)

  2. Cancerology: to see and to treat with molecular imaging

    International Nuclear Information System (INIS)

    2004-01-01

    By allowing to visualize, beyond the organs and tissues structure, the molecules present inside cells and their action in cell functioning, to the genome level, the molecular imaging opens a new era in biology and medicine and creates the conditions for the perfecting of targeting and personalised treatments of cancers. The E.M.I.L. network is the only European network in molecular imaging for the cancer. It has been initiated and is coordinated by 'the genes expression in vivo imaging group' of the Cea at Orsay. The E.M.I.L network represents 43 organisms of 13 european countries with 6 technological platforms. (N.C.)

  3. Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Niklasson, Anders M N

    2012-10-07

    Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

  4. Femtochemistry and femtobiology ultrafast dynamics in molecular science

    CERN Document Server

    Douhal, Abderrazzak

    2002-01-01

    This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

  5. AceCloud: Molecular Dynamics Simulations in the Cloud.

    Science.gov (United States)

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  6. State-to-state dynamics of molecular energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  7. Chain networking revealed by molecular dynamics simulation

    Science.gov (United States)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  8. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-01-01

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

  9. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    National Research Council Canada - National Science Library

    Hong, Waun Ki; Herbst, Roy

    2006-01-01

    .... These projects combine targeted approaches using molecular and imaging techniques to validate activity against a target and monitor response using imaging modalities specific to the receptor using...

  10. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    National Research Council Canada - National Science Library

    Hong, Waun K; Herbst, Roy

    2008-01-01

    .... These projects combine targeted approaches using molecular and imaging techniques to validate activity against a target and monitor response using imaging modalities specific to the receptor using...

  11. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    National Research Council Canada - National Science Library

    Hong, Waun K; Herbst, Roy

    2007-01-01

    .... These projects combine targeted approaches using molecular and imaging techniques to validate activity against a target and monitor response using imaging modalities specific to the receptor using...

  12. [Future perspectives for diagnostic imaging in urology: from anatomic and functional to molecular imaging].

    Science.gov (United States)

    Macis, Giuseppe; Di Giovanni, Silvia; Di Franco, Davide; Bonomo, Lorenzo

    2013-01-01

    The future approach of diagnostic imaging in urology follows the technological progress, which made the visualization of in vivo molecular processes possible. From anatomo-morphological diagnostic imaging and through functional imaging molecular radiology is reached. Based on molecular probes, imaging is aimed at assessing the in vivo molecular processes, their physiology and function at cellular level. The future imaging will investigate the complex tumor functioning as metabolism, aerobic glycolysis in particular, angiogenesis, cell proliferation, metastatic potential, hypoxia, apoptosis and receptors expressed by neoplastic cells. Methods for performing molecular radiology are CT, MRI, PET-CT, PET-MRI, SPECT and optical imaging. Molecular ultrasound combines technological advancement with targeted contrast media based on microbubbles, this allowing the selective registration of microbubble signal while that of stationary tissues is suppressed. An experimental study was carried out where the ultrasound molecular probe BR55 strictly bound to prostate tumor results in strong enhancement in the early phase after contrast, this contrast being maintained in the late phase. This late enhancement is markedly significant for the detection of prostatic cancer foci and to guide the biopsy sampling. The 124I-cG250 molecular antibody which is strictly linked to cellular carbonic anhydrase IX of clear cell renal carcinoma, allows the acquisition of diagnostic PET images of clear cell renal carcinoma without biopsy. This WG-250 (RENCAREX) antibody was used as a therapy in metastatic clear cell renal carcinoma. Future advancements and applications will result in early cancer diagnosis, personalized therapy that will be specific according to the molecular features of cancer and leading to the development of catheter-based multichannel molecular imaging devices for cystoscopy-based molecular imaging diagnosis and intervention.

  13. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  14. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-01-01

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition

  15. Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

    Czech Academy of Sciences Publication Activity Database

    Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

    2015-01-01

    Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

  16. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.

    1991-01-01

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  17. Dynamic MR imaging of mandibular osteoradionecrosis

    International Nuclear Information System (INIS)

    Store, G.; Smith, H.J.; Larheim, T.A.

    2000-01-01

    Osteoradionecrotic bone has been characterised as hypovascular and metabolically inactive tissue with impaired perfusion. The present study was conducted to determine if dynamic contrast-enhanced MR imaging could provide additional information about the vascularity of radionecrotic mandibular bone. Dynamic contrast-enhanced MR imaging was performed on 10 patients with mandibular osteoradionecrosis (ORN), and on 6 patients, irradiated for oropharyngeal tumours, without symptoms or signs of ORN. Nine patients in the ORN group received a series of 20 hyperbaric oxygen (HBO) treatments, after which the dynamic MR investigation was repeated. Radiation per se did not lead to increased contrast enhancement, whereas all patients with ORN showed marked contrast enhancement of the osteoradionecrotic bone marrow. After HBO treatment, pathological contrast enhancement of the abnormal bone marrow could still be seen, but the rate of enhancement was less than before in 7 of 9 patients. Two patients had an increase in the enhancement rate. The findings suggest the existence of an increased and patent microvasculature

  18. Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    Energy Technology Data Exchange (ETDEWEB)

    Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)

    2015-08-18

    Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

  19. Thermoacoustic Molecular Imaging of Small Animals

    Directory of Open Access Journals (Sweden)

    Robert A. Kruger

    2003-04-01

    Full Text Available We have designed, constructed, and tested a thermoacoustic computed tomography (TCT scanner for imaging optical absorption in small animals in three dimensions. The device utilizes pulsed laser irradiation (680–1064 nm and a unique, 128-element transducer array. We quantified the isotropic spatial resolution of this scanner to be 0.35 mm. We describe a dual-wavelength subtraction technique for isolating optical dyes with TCT. Phantom experiments demonstrate that we can detect 5 fmol of a near-infrared dye (indocyanine green, ICG in a 1-ML volume using dual-wavelength subtraction. Initial TCT imaging in phantoms and in two sacrificed mice suggests that three-dimensional, optical absorption patterns in small animals can be detected with an order of magnitude better spatial resolution and an order of magnitude better low-contrast detectability in small animals when compared to fluorescence imaging or diffusion optical tomography.

  20. Theory of multiexciton dynamics in molecular chains

    Science.gov (United States)

    Wang, Luxia; May, Volkhard

    2016-11-01

    Ultrafast and strong optical excitation of a molecular system is considered which is formed by a regular one-dimensional arrangement of identical molecules. As it is typical for zinc chlorine-type molecules the transition energy from the ground state to the first excited singlet state is assumed to be smaller than the energy difference between the first excited state and the following one. This enables the creation of many excitons without their immediate quenching due to exciton-exciton annihilation. As a first step into the field of dense Frenkel-exciton systems the present approach stays at a mean-field type of description and ignores vibrational contributions. The resulting nonlinear kinetic equations mix Rabi-type oscillations with those caused by energy transfer and suggest an excitation-dependent narrowing of the exciton band. The indication of this effect in the framework of a two-color pump-probe experiment and of the detection of photon emission is discussed.

  1. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  2. Direct reconstruction of pharmacokinetic parameters in dynamic fluorescence molecular tomography by the augmented Lagrangian method

    Science.gov (United States)

    Zhu, Dianwen; Zhang, Wei; Zhao, Yue; Li, Changqing

    2016-03-01

    Dynamic fluorescence molecular tomography (FMT) has the potential to quantify physiological or biochemical information, known as pharmacokinetic parameters, which are important for cancer detection, drug development and delivery etc. To image those parameters, there are indirect methods, which are easier to implement but tend to provide images with low signal-to-noise ratio, and direct methods, which model all the measurement noises together and are statistically more efficient. The direct reconstruction methods in dynamic FMT have attracted a lot of attention recently. However, the coupling of tomographic image reconstruction and nonlinearity of kinetic parameter estimation due to the compartment modeling has imposed a huge computational burden to the direct reconstruction of the kinetic parameters. In this paper, we propose to take advantage of both the direct and indirect reconstruction ideas through a variable splitting strategy under the augmented Lagrangian framework. Each iteration of the direct reconstruction is split into two steps: the dynamic FMT image reconstruction and the node-wise nonlinear least squares fitting of the pharmacokinetic parameter images. Through numerical simulation studies, we have found that the proposed algorithm can achieve good reconstruction results within a small amount of time. This will be the first step for a combined dynamic PET and FMT imaging in the future.

  3. Molecular Imaging in Stem Cell Therapy for Spinal Cord Injury

    Directory of Open Access Journals (Sweden)

    Fahuan Song

    2014-01-01

    Full Text Available Spinal cord injury (SCI is a serious disease of the center nervous system (CNS. It is a devastating injury with sudden loss of motor, sensory, and autonomic function distal to the level of trauma and produces great personal and societal costs. Currently, there are no remarkable effective therapies for the treatment of SCI. Compared to traditional treatment methods, stem cell transplantation therapy holds potential for repair and functional plasticity after SCI. However, the mechanism of stem cell therapy for SCI remains largely unknown and obscure partly due to the lack of efficient stem cell trafficking methods. Molecular imaging technology including positron emission tomography (PET, magnetic resonance imaging (MRI, optical imaging (i.e., bioluminescence imaging (BLI gives the hope to complete the knowledge concerning basic stem cell biology survival, migration, differentiation, and integration in real time when transplanted into damaged spinal cord. In this paper, we mainly review the molecular imaging technology in stem cell therapy for SCI.

  4. Magnetic nanoparticles as contrast agents for molecular imaging in medicine

    Science.gov (United States)

    O'Donnell, Matthew

    2018-05-01

    For over twenty years, superparamagnetic nanoparticles have been developed for a number of medical applications ranging from bioseparations, magnetic drug targeting, hyperthermia and imaging. Recent studies have shown that they can be functionalized for in vivo biological targeting, potentially enabling nanoagents for molecular imaging and site-localized drug delivery. Here we review several imaging technologies developed using functionalized superparamagnetic iron oxide nanoparticles (SPIONs) as targeted molecular agents. Several imaging modalities have exploited the large induced magnetic moment of SPIONs to create local mechanical force. Magnetic force microscopy can probe nanoparticle uptake in single cells. For in vivo applications, magnetomotive modulation of primary images in ultrasound (US), photoacoustics (PA), and optical coherence tomography (OCT) can help identify very small concentrations of nanoagents while simultaneously suppressing intrinsic background signals from tissue.

  5. Multi-target molecular imaging and its progress in research and application

    International Nuclear Information System (INIS)

    Tang Ganghua

    2011-01-01

    Multi-target molecular imaging (MMI) is an important field of research in molecular imaging. It includes multi-tracer multi-target molecular imaging(MTMI), fusion-molecule multi-target imaging (FMMI), coupling-molecule multi-target imaging (CMMI), and multi-target multifunctional molecular imaging(MMMI). In this paper,imaging modes of MMI are reviewed, and potential applications of positron emission tomography MMI in near future are discussed. (author)

  6. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  7. Photoionization dynamics of excited molecular states

    International Nuclear Information System (INIS)

    Dehmer, J.L.; O'Halloran, M.A.; Tomkins, F.S.; Dehmer, P.M.; Pratt, S.T.

    1987-01-01

    Resonance Enhanced Multiphoton Ionization (REMPI) utilizes tunable dye lasers to ionize an atom or molecule by first preparing an excited state by multiphoton absorption and then ionizing that state before it can decay. This process is highly selective with respect to both the initial and resonant intermediate states of the target, and it can be extremely sensitive. In addition, the products of the REMPI process can be detected as needed by analyzing the resulting electrons, ions, fluorescence, or by additional REMPI. This points to a number of opportunities for exploring excited state physics and chemistry at the quantum-state-specific level. Here we will first give a brief overview of the large variety of experimental approaches to excited state phenomena made possible by REMPI. Then we will examine in more detail, recent studies of the three photon resonant, four photon (3 + 1) ionization of H 2 via the C 'PI/sup u/ state. Strong non-Franck-Condon behavior in the photoelectron spectra of this nominally simple Rydberg state has led to the examination of a variety of dynamical mechanisms. Of these, the role of doubly excited autoionizing states now seems decisive. Progress on photoelectron studies of autoionizing states in H 2 , excited in a (2 + 1) REMPI process via the E, F 1 Σ/sub g/ + will also be briefly discussed. 26 refs., 7 figs

  8. Solar Flare Dynamic Microwave Imaging with EOVSA

    Science.gov (United States)

    Gary, D. E.; Chen, B.; Nita, G. M.; Fleishman, G. D.; Yu, S.; White, S. M.; Hurford, G. J.; McTiernan, J. M.

    2017-12-01

    The Expanded Owens Valley Solar Array (EOVSA) is both an expansion of our existing solar array and serves as a prototype for a much larger future project, the Frequency Agile Solar Radiotelescope (FASR). EOVSA is now complete, and is producing daily imaging of the full solar disk, including active regions and solar radio bursts at hundreds of frequencies in the range 2.8-18 GHz. We present highlights of the 1-s-cadence dynamic imaging spectroscropy of radio bursts we have obtained to date, along with deeper analysis of multi-wavelength observations and modeling of a well-observed burst. These observations are revealing the full life-cycle of the trapped population of high-energy electrons, from their initial acceleration and subsequent energy-evolution to their eventual decay through escape and thermalization. All of our data are being made available for download in both quick-look image form and in the form of the community-standard CASA measurement sets for subsequent imaging and analysis.

  9. Dynamical photo-induced electronic properties of molecular junctions

    Science.gov (United States)

    Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

    2018-03-01

    Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

  10. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...

  11. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  12. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    NARCIS (Netherlands)

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

    Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

  13. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  14. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  15. Microsecond atomic-scale molecular dynamics simulations of polyimides

    NARCIS (Netherlands)

    Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

    2013-01-01

    We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

  16. Molecular dynamics study of the silica-water-SDA interactions

    NARCIS (Netherlands)

    Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.

    2009-01-01

    In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species

  17. Molecular dynamics simulations of ballistic He penetration into W fuzz

    NARCIS (Netherlands)

    Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

    2016-01-01

    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers

  18. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2015-01-01

    Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  19. Toluene model for molecular dynamics simulations in the ranges 298

    NARCIS (Netherlands)

    Fioroni, M.; Vogt, D.

    2004-01-01

    An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons

  20. Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics

    NARCIS (Netherlands)

    Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de

    1997-01-01

    The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.

  1. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

  2. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  3. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  4. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  5. Molecular dynamics study on the relaxation properties of bilayered ...

    Indian Academy of Sciences (India)

    2017-08-31

    Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

  6. Metal cluster fission: jellium model and Molecular dynamics simulations

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...

  7. Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

    Indian Academy of Sciences (India)

    Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

  8. Free energy from molecular dynamics with multiple constraints

    NARCIS (Netherlands)

    den Otter, Wouter K.; Briels, Willem J.

    2000-01-01

    In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

  9. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  10. Time-resolved imaging of purely valence-electron dynamics during a chemical reaction

    DEFF Research Database (Denmark)

    Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.

    2011-01-01

    Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods...... such as electron(7-10) or X-ray diffraction(11) and X-ray absorption(12) yield complementary information about the atomic motions. Time-resolved methods that are directly sensitive to both valence-electron dynamics and atomic motions include photoelectron spectroscopy(13-15) and high-harmonic generation(16......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...

  11. Harnessing Integrative Omics to Facilitate Molecular Imaging of the Human Epidermal Growth Factor Receptor Family for Precision Medicine.

    Science.gov (United States)

    Pool, Martin; de Boer, H Rudolf; Hooge, Marjolijn N Lub-de; van Vugt, Marcel A T M; de Vries, Elisabeth G E

    2017-01-01

    Cancer is a growing problem worldwide. The cause of death in cancer patients is often due to treatment-resistant metastatic disease. Many molecularly targeted anticancer drugs have been developed against 'oncogenic driver' pathways. However, these treatments are usually only effective in properly selected patients. Resistance to molecularly targeted drugs through selective pressure on acquired mutations or molecular rewiring can hinder their effectiveness. This review summarizes how molecular imaging techniques can potentially facilitate the optimal implementation of targeted agents. Using the human epidermal growth factor receptor (HER) family as a model in (pre)clinical studies, we illustrate how molecular imaging may be employed to characterize whole body target expression as well as monitor drug effectiveness and the emergence of tumor resistance. We further discuss how an integrative omics discovery platform could guide the selection of 'effect sensors' - new molecular imaging targets - which are dynamic markers that indicate treatment effectiveness or resistance.

  12. Molecular imaging: a new approach to nuclear cardiology

    International Nuclear Information System (INIS)

    Dobrucki, L.W.; Sinusas, A.J.

    2005-01-01

    Nuclear cardiology has historically played an important role in detection of cardiovascular disease as well as risk statification. With the growth of molecular biology have come new therapeutic interventions and the requirement for new diagnostic imaging approaches. Noninvasive targeted radiotracer based as well as transporter gene imaging strategies are evolving to meet these new needs, but require the development of an interdisciplinary approach which focuses on molecular processes, as well as the pathogenesis and progression of disease. This progress has been made possible with the availability of transgenic animal models along with many technological advances. Future adaptations of the developing experimental procedures and instrumentations will allow for the smooth translation and application to clinical practice. This review is intended as a brief overview on the subject molecular imaging. Basic concepts and historical perspective of molecular imaging will be reviewed first, followed by description of current technology, and concluding with current applications in cardiology. The emphasis will be on the use of both single photon emission computed tomography (SPECT) and positron emission tomography (PET) radiotracers, although other imaging modalities will be also briefly discussed. The specific approaches presented here will include receptor-based and reporter gene imaging of natural and therapeutical angiogenesis

  13. High dynamic range image acquisition based on multiplex cameras

    Science.gov (United States)

    Zeng, Hairui; Sun, Huayan; Zhang, Tinghua

    2018-03-01

    High dynamic image is an important technology of photoelectric information acquisition, providing higher dynamic range and more image details, and it can better reflect the real environment, light and color information. Currently, the method of high dynamic range image synthesis based on different exposure image sequences cannot adapt to the dynamic scene. It fails to overcome the effects of moving targets, resulting in the phenomenon of ghost. Therefore, a new high dynamic range image acquisition method based on multiplex cameras system was proposed. Firstly, different exposure images sequences were captured with the camera array, using the method of derivative optical flow based on color gradient to get the deviation between images, and aligned the images. Then, the high dynamic range image fusion weighting function was established by combination of inverse camera response function and deviation between images, and was applied to generated a high dynamic range image. The experiments show that the proposed method can effectively obtain high dynamic images in dynamic scene, and achieves good results.

  14. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  15. Multiscale equation-free algorithms for molecular dynamics

    Science.gov (United States)

    Abi Mansour, Andrew

    Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

  16. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  17. Molecular Imaging of Ovarian Carcinoma Angiogenesis

    Science.gov (United States)

    2007-03-01

    specifically taken up by several benign conditions such as inflammatory disease, pneumonia, brown fat, muscle, bowel uptake, and granulomatous disease...demonstrated in vivo imaging of vascular cell proliferation- associated states, whether focal, as in postangioplasty re- stenosis , or diffuse, as in pulmonary...limitations. The tracer can be nonspecifically taken up by several benign condi- tions such as inflammatory disease, pneumonia, brown fat, muscle

  18. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

  19. Implementation of surface hopping molecular dynamics using semiempirical methods

    International Nuclear Information System (INIS)

    Fabiano, E.; Keal, T.W.; Thiel, W.

    2008-01-01

    A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

  20. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  1. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

    Science.gov (United States)

    Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

    2015-04-21

    Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

  2. Molecular Imaging of Breast Cancer: Present and future directions

    Directory of Open Access Journals (Sweden)

    David eAlcantara

    2014-12-01

    Full Text Available Medical imaging technologies have undergone explosive growth over the past few decades and now play a central role in clinical oncology. But the truly transformative power of imaging in the clinical management of cancer patients lies ahead. Today, imaging is at a crossroads, with molecularly targeted imaging agents expected to broadly expand the capabilities of conventional anatomical imaging methods. Molecular imaging will allow clinicians to not only see where a tumour is located in the body, but also to visualize the expression and activity of specific molecules (e.g. proteases and protein kinases and biological processes (e.g. apoptosis, angiogenesis, and metastasis that influence tumour behavior and/or response to therapy. Breast cancer, the most common cancer among women and a research area where our group is actively involved, is a very heterogeneous disease with diverse patterns of development and response to treatment. Hence, molecular imaging is expected to have a major impact on this type of cancer, leading to important improvements in diagnosis, individualized treatment, and drug development, as well as our understanding of how breast cancer arises.

  3. Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm.

    Science.gov (United States)

    Vargas, Hebert Alberto; Grimm, Jan; F Donati, Olivio; Sala, Evis; Hricak, Hedvig

    2015-05-01

    The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. • Advanced imaging techniques allow direct visualisation of molecular interactions in prostate cancer. • MRI/PET, optical and Cerenkov imaging facilitate the translation of molecular biology. • Multiple compounds targeting PSMA expression are currently undergoing clinical translation. • Other targets (e.g., PSA, prostate-stem cell antigen, GRPR) are in development.

  4. Molecular magnetic resonance imaging of atherosclerotic vessel wall disease

    Energy Technology Data Exchange (ETDEWEB)

    Noerenberg, Dominik [Charite - University Medicine Berlin, Department of Radiology, Berlin (Germany); University of Munich - Grosshadern, Department of Clinical Radiology, Munich (Germany); Ebersberger, Hans U. [Heart Center Munich-Bogenhausen, Department of Cardiology and Intensive Care Medicine, Munich (Germany); Diederichs, Gerd; Hamm, Bernd [Charite - University Medicine Berlin, Department of Radiology, Berlin (Germany); Botnar, Rene M. [King' s College London, Division of Imaging Sciences and Biomedical Engineering, London (United Kingdom); Makowski, Marcus R. [Charite - University Medicine Berlin, Department of Radiology, Berlin (Germany); King' s College London, Division of Imaging Sciences and Biomedical Engineering, London (United Kingdom)

    2016-03-15

    Molecular imaging aims to improve the identification and characterization of pathological processes in vivo by visualizing the underlying biological mechanisms. Molecular imaging techniques are increasingly used to assess vascular inflammation, remodeling, cell migration, angioneogenesis and apoptosis. In cardiovascular diseases, molecular magnetic resonance imaging (MRI) offers new insights into the in vivo biology of pathological vessel wall processes of the coronary and carotid arteries and the aorta. This includes detection of early vascular changes preceding plaque development, visualization of unstable plaques and assessment of response to therapy. The current review focuses on recent developments in the field of molecular MRI to characterise different stages of atherosclerotic vessel wall disease. A variety of molecular MR-probes have been developed to improve the non-invasive detection and characterization of atherosclerotic plaques. Specifically targeted molecular probes allow for the visualization of key biological steps in the cascade leading to the development of arterial vessel wall lesions. Early detection of processes which lead to the development of atherosclerosis and the identification of vulnerable atherosclerotic plaques may enable the early assessment of response to therapy, improve therapy planning, foster the prevention of cardiovascular events and may open the door for the development of patient-specific treatment strategies. (orig.)

  5. Molecular magnetic resonance imaging of atherosclerotic vessel wall disease

    International Nuclear Information System (INIS)

    Noerenberg, Dominik; Ebersberger, Hans U.; Diederichs, Gerd; Hamm, Bernd; Botnar, Rene M.; Makowski, Marcus R.

    2016-01-01

    Molecular imaging aims to improve the identification and characterization of pathological processes in vivo by visualizing the underlying biological mechanisms. Molecular imaging techniques are increasingly used to assess vascular inflammation, remodeling, cell migration, angioneogenesis and apoptosis. In cardiovascular diseases, molecular magnetic resonance imaging (MRI) offers new insights into the in vivo biology of pathological vessel wall processes of the coronary and carotid arteries and the aorta. This includes detection of early vascular changes preceding plaque development, visualization of unstable plaques and assessment of response to therapy. The current review focuses on recent developments in the field of molecular MRI to characterise different stages of atherosclerotic vessel wall disease. A variety of molecular MR-probes have been developed to improve the non-invasive detection and characterization of atherosclerotic plaques. Specifically targeted molecular probes allow for the visualization of key biological steps in the cascade leading to the development of arterial vessel wall lesions. Early detection of processes which lead to the development of atherosclerosis and the identification of vulnerable atherosclerotic plaques may enable the early assessment of response to therapy, improve therapy planning, foster the prevention of cardiovascular events and may open the door for the development of patient-specific treatment strategies. (orig.)

  6. Dislocation-cavity interaction in Fe: a comparison between molecular dynamics and dislocation dynamics

    International Nuclear Information System (INIS)

    Hafez Haghighat, S.M.; Schaeublin, R.; Fivel, M.C.

    2007-01-01

    Full text of publication follows: multi-scale modeling, including molecular dynamics (MD) and discrete dislocation dynamics (DDD) methods, appears as a significant tool for the description of plasticity and mechanical properties of materials. This research is on the investigation of the subsequence effects of irradiation on the plasticity of pure Fe and focuses on the interaction of a single dislocation and a spherical cavity, as void or He bubble. Extensive MD simulations of the interaction under imposed strain rate [1, 2] have shown that various temperatures and cavity sizes result in different release stresses depending on dislocation bow out. It appears that a temperature increase and cavity size decrease reduce the cavity strength. MD simulation shows that the elastic field around the cavity is largely anisotropic. This anisotropy may influence the way the dislocation unpins from the cavity. Following the MD simulations, the interaction of a single dislocation and a spherical cavity is now simulated using a DDD discrete dislocation dynamics model. The simulation accounts for the non-Schmidt effect induced by the bcc structure of Fe through local rules derived from MD simulations [3]. The cavity is introduced in the simulation by computing the image forces using a finite element technique. The effective stress applied on the dislocation is then obtained as the superimposition of the applied stress field, the image stress field and the internal stresses. Note that such a model only uses elasticity theory and no core effect of dislocations is taken into account. One of the objectives of this work is to check whether elasticity is responsible of the behaviour observed by MD. Several cases are tested. First an edge dislocation in a (110) plane is pushed against the cavity under a pure shear loading. The local reaction of the dislocations and the cavity are compared to the MD simulations. Then, the case of a screw dislocation is studied. Finally, other loading

  7. Multimodality molecular imaging - from target description to clinical studies

    International Nuclear Information System (INIS)

    Schober, O.; Rahbar, K.; Riemann, B.

    2009-01-01

    This highlight lecture was presented at the closing session of the Annual Congress of the European Association of Nuclear Medicine (EANM) in Munich on 15 October 2008. The Congress was a great success: there were more than 4,000 participants, and 1,597 abstracts were submitted. Of these, 1,387 were accepted for oral or poster presentation, with a rejection rate of 14%. In this article a choice was made from 100 of the 500 lectures which received the highest scores by the scientific review panel. This article outlines the major findings and trends at the EANM 2008, and is only a brief summary of the large number of outstanding abstracts presented. Among the great number of oral and poster presentations covering nearly all fields of nuclear medicine some headlines have to be defined highlighting the development of nuclear medicine in the 21st century. This review focuses on the increasing impact of molecular and multimodality imaging in the field of nuclear medicine. In addition, the question may be asked as to whether the whole spectrum of nuclear medicine is nothing other than molecular imaging and therapy. Furthermore, molecular imaging will and has to go ahead to multimodality imaging. In view of this background the review was structured according to the single steps of molecular imaging, i.e. from target description to clinical studies. The following topics are addressed: targets, radiochemistry and radiopharmacy, devices and computer science, animals and preclinical evaluations, and patients and clinical evaluations. (orig.)

  8. Ultrafast molecular imaging by laser-induced electron diffraction

    International Nuclear Information System (INIS)

    Peters, M.; Nguyen-Dang, T. T.; Cornaggia, C.; Saugout, S.; Charron, E.; Keller, A.; Atabek, O.

    2011-01-01

    We address the feasibility of imaging geometric and orbital structures of a polyatomic molecule on an attosecond time scale using the laser-induced electron diffraction (LIED) technique. We present numerical results for the highest molecular orbitals of the CO 2 molecule excited by a near-infrared few-cycle laser pulse. The molecular geometry (bond lengths) is determined within 3% of accuracy from a diffraction pattern which also reflects the nodal properties of the initial molecular orbital. Robustness of the structure determination is discussed with respect to vibrational and rotational motions with a complete interpretation of the laser-induced mechanisms.

  9. Advances in study of molecular imaging reporte gene systems

    International Nuclear Information System (INIS)

    Wu Tao; An Rui

    2010-01-01

    The use of molecular imaging reporter gene systems has allowed gene therapy to move from the laboratory to the clinical application, which provides methodology to monitor the expression of therapeutic gene noninvasively and achieve quantitative outcome in vivo. Recently, the radionuclide reporter gene still is the focus many studies, but MRI and optical reporter gene have gradually played a important part in reporter gene systems. On the basis of combination of multi-subject, for example applied chemistry and molecular biology, more and more new modified reporter genes and molecular probes have spread out. This paper mainly introduces the advantages and disadvantages of reporter gene system and development trends. (authors)

  10. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik; Szepessy, Anders

    2010-01-01

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  11. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  12. Molecular electron recollision dynamics in intense circularly polarized laser pulses

    Science.gov (United States)

    Bandrauk, André D.; Yuan, Kai-Jun

    2018-04-01

    Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

  13. Development of molecular imaging in the European radiological community

    International Nuclear Information System (INIS)

    Grenier, Nicolas; Sardanelli, Francesco; Becker, Christoph D.; Walecki, Jerzy; Sebag, Guy; Lomas, David John; Krestin, Gabriel P.

    2009-01-01

    The recent and concomitant advances in molecular biology and imaging for diagnosis and therapy will place in vivo imaging techniques at the centre of their clinical transfer. Before that, a wide range of multidisciplinary preclinical research is already taking place. The involvement of radiologists in this new field of imaging sciences is therefore absolutely mandatory during these two phases of development. Achievement of such objectives requires the refinement of strategy within the European radiological community and the European Society of Radiology (ESR) will have to drive a number of actions to stimulate the younger generation of radiologists and to facilitate their access to knowledge. For that purpose, a molecular imaging (MI) subcommittee of the ESR Research Committee based on a group of involved radiologists will be constituted to develop contacts with other constitutive committees and associated societies to provide proposals to our community. (orig.)

  14. Molecular Imaging with Small Animal PET/CT

    DEFF Research Database (Denmark)

    Binderup, T.; El-Ali, H.H.; Skovgaard, D.

    2011-01-01

    is also described. In addition, the non-invasive nature of molecular imaging and the targets of these promising new tracers are attractive for other research areas as well, although these fields are much less explored. We present an example of an interesting research field with the application of small......Small animal positron emission tomography (PET) and computer tomography (CT) is an emerging field in pre-clinical imaging. High quality, state-of-the-art instruments are required for full optimization of the translational value of the small animal studies with PET and CT. However...... in this field of small animal molecular imaging with special emphasis on the targets for tissue characterization in tumor biology such as hypoxia, proliferation and cancer specific over-expression of receptors. The added value of applying CT imaging for anatomical localization and tumor volume measurements...

  15. [Microdose clinical trial--impact of PET molecular imaging].

    Science.gov (United States)

    Yano, Tsuneo; Watanabe, Yasuyoshi

    2010-10-01

    Microdose (MD) clinical trial and exploratory IND study including sub-therapeutic dose and therapeutic dose which are higher than microdoses are expected to bring about innovations in drug development. The outlines of guidances for microdose clinical trial and ICH-M3 (R2) issued by the MHLW in June, 2008, and February, 2010, are first explained, respectively, and some examples of their application to clinical developments of therapeutic drugs in the infection and cancer fields are introduced. Especially, thanks to the progress of molecular imaging research, a new field of drug development is explored by using imaging biomarkers for efficacy or safety evaluation which visualize biomarkers by PET imaging agents. Finally, the roadmap for drug development in infection and cancer fields utilizing PET molecular imaging is discussed.

  16. Molecular Imaging: A Promising Tool to Monitor Islet Transplantation

    Directory of Open Access Journals (Sweden)

    Ping Wang

    2011-01-01

    Full Text Available Replacement of insulin production by pancreatic islet transplantation has great potential as a therapy for type 1 diabetes mellitus. At present, the lack of an effective approach to islet grafts assessment limits the success of this treatment. The development of molecular imaging techniques has the potential to fulfill the goal of real-time noninvasive monitoring of the functional status and viability of the islet grafts. We review the application of a variety of imaging modalities for detecting endogenous and transplanted beta-cell mass. The review also explores the various molecular imaging strategies for assessing islet delivery, the metabolic effects on the islet grafts as well as detection of immunorejection. Here, we highlight the use of combined imaging and therapeutic interventions in islet transplantation and the in vivo monitoring of stem cells differentiation into insulin-producing cells.

  17. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

    Science.gov (United States)

    2014-01-01

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

  18. Simultaneous molecular and anatomical imaging of the mouse in vivo

    International Nuclear Information System (INIS)

    Goertzen, Andrew L; Meadors, A Ken; Silverman, Robert W; Cherry, Simon R

    2002-01-01

    Non-invasive imaging technologies are opening up new windows into mouse biology. We have developed a mouse imaging system that integrates positron emission tomography (PET) with x-ray computed tomography (CT), allowing simultaneous anatomic and molecular imaging in vivo with the potential for precise registration of the two image volumes. The x-ray system consists of a compact mini-focal x-ray tube and an amorphous selenium flat panel x-ray detector with a low-noise CMOS readout. The PET system uses planar arrays of lutetium oxyorthosilicate scintillator coupled to position-sensitive photomultiplier tubes. We describe the design of this dual-modality imaging system and show, for the first time, simultaneously acquired PET and CT images in a phantom and in mice

  19. Simultaneous molecular and anatomical imaging of the mouse in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Goertzen, Andrew L [Crump Institute for Molecular Imaging, David Geffen School of Medicine at UCLA, Los Angeles, CA (United States); Meadors, A Ken [Crump Institute for Molecular Imaging, David Geffen School of Medicine at UCLA, Los Angeles, CA (United States); Silverman, Robert W [Crump Institute for Molecular Imaging, David Geffen School of Medicine at UCLA, Los Angeles, CA (United States); Cherry, Simon R [Department of Biomedical Engineering, University of California, Davis, Davis, CA (United States)

    2002-12-21

    Non-invasive imaging technologies are opening up new windows into mouse biology. We have developed a mouse imaging system that integrates positron emission tomography (PET) with x-ray computed tomography (CT), allowing simultaneous anatomic and molecular imaging in vivo with the potential for precise registration of the two image volumes. The x-ray system consists of a compact mini-focal x-ray tube and an amorphous selenium flat panel x-ray detector with a low-noise CMOS readout. The PET system uses planar arrays of lutetium oxyorthosilicate scintillator coupled to position-sensitive photomultiplier tubes. We describe the design of this dual-modality imaging system and show, for the first time, simultaneously acquired PET and CT images in a phantom and in mice.

  20. Usefulness of dynamic magnetic resonance imaging in pituitary microadenomas

    International Nuclear Information System (INIS)

    Rhee, Chang Soo; Lee, Eun Young; Joo, Yang Gu; Kim, Hong; Lee, Hee Jung; Sch, Soo Ji

    1996-01-01

    To investigate the usefulness of dynamic MR imaging in the diagnosis of pituitary microadenomas. Dynamic MR imaging was performed in 31 patients with suspicious pituitary microadinoma. The MR examination was performed on a 2.0T or 1.5T superconductive MR unit using spin echo(SE) technique with a repetition time of 200msec, echo time of 15 msec, 128X256 matrix and one excitation. Actual sampling time per image was 26 seconds. The field of view was 25cm and a section thickness if 3 mm with 2mm gap was chose. After a rapid hand injection(2-3ml/sec) of Gd-DTPA(0.1 mmol/kg of body weight), dynamic coronal plane MR images were obtained every 20-30 seconds for 3-5 minutes. Between never and ten serial images were usually obtained. After dynamic MR imaging, toutine SE T1-weighted images(T1W1) were obtained in the same plane as dynamic images, and detection rates of pituitary microadinoma using dynamic MR imaging and using routine enhanced T1W1, were retrospectively compared. On early dynamic images(30-90 seconds), 23 of 31 adenomas(74.2%) were well visualized at 30-second dynamic image. On late dynamic images(120-180 seconds), six microadeomas(19.4%) were well-visualized and ; two(6.5%) were well-visualized on toutine Gd-DTPA enhanced T1W1. dynamic MR imaging with Gd-DTPA bolus injection was the most useful technique for the detection of pituitary microadenoma, especially on early-phase dynamic images

  1. Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

    Science.gov (United States)

    Cooke, Ben; Schmidler, Scott C

    2008-10-28

    We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

  2. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F

    2007-08-15

    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  3. Molecular imaging of small animals with dedicated PET tomographs

    International Nuclear Information System (INIS)

    Chatziioannou, A.F.

    2002-01-01

    Biological discovery has moved at an accelerated pace in recent years, with a considerable focus on the transition from in vitro to in vivo models. As a result, there has been a significant increase in the need to adapt clinical imaging methods, as well as for novel imaging technologies for biological research. Positron emission tomography (PET) is a clinical imaging modality that permits the use of positron-labeled molecular imaging probes for non-invasive assays of biochemical processes. The imaging procedure can be repeatedly performed before and after interventions, thereby allowing each animal to be used as its own control. Positron-labeled compounds that target a range of molecular targets have been and continue to be synthesized, with examples of biological processes ranging from receptors and synthesis of transmitters in cell communication, to metabolic processes and gene expression. In animal research, PET has been used extensively in the past for studies of non-human primates and other larger animals. New detector technology has improved spatial resolution, and has made possible PET scanning for the study of the most important modern molecular biology model, the laboratory mouse. This paper presents the challenges facing PET technology as applied to small animal imaging, provides a historical overview of the development of small animal PET systems, and discusses the current state of the art in small animal PET technology. (orig.)

  4. Nonlinear microrheology and molecular imaging to map microscale deformations of entangled DNA networks

    Science.gov (United States)

    Wu, Tsai-Chin; Anderson, Rae

    We use active microrheology coupled to single-molecule fluorescence imaging to elucidate the microscale dynamics of entangled DNA. DNA naturally exists in a wide range of lengths and topologies, and is often confined in cell nucleui, forming highly concentrated and entangled biopolymer networks. Thus, DNA is the model polymer for understanding entangled polymer dynamics as well as the crowded environment of cells. These networks display complex viscoelastic properties that are not well understood, especially at the molecular-level and in response to nonlinear perturbations. Specifically, how microscopic stresses and strains propagate through entangled networks, and what molecular deformations lead to the network stress responses are unknown. To answer these important questions, we optically drive a microsphere through entangled DNA, perturbing the system far from equilibrium, while measuring the resistive force the DNA exerts on the bead during and after bead motion. We simultaneously image single fluorescent-labeled DNA molecules throughout the network to directly link the microscale stress response to molecular deformations. We characterize the deformation of the network from the molecular-level to the mesoscale, and map the stress propagation throughout the network. We further study the impact of DNA length (11 - 115 kbp) and topology (linear vs ring DNA) on deformation and propagation dynamics, exploring key nonlinear features such as tube dilation and power-law relaxation.

  5. Tracking nuclear wave-packet dynamics in molecular oxygen ions with few-cycle infrared laser pulses

    International Nuclear Information System (INIS)

    De, S.; Bocharova, I. A.; Magrakvelidze, M.; Ray, D.; Cao, W.; Thumm, U.; Cocke, C. L.; Bergues, B.; Kling, M. F.; Litvinyuk, I. V.

    2010-01-01

    We have tracked nuclear wave-packet dynamics in doubly charged states of molecular oxygen using few-cycle infrared laser pulses. Bound and dissociating wave packets were launched and subsequently probed via a pair of 8-fs pulses of 790 nm radiation. Ionic fragments from the dissociating molecules were monitored by velocity-map imaging. Pronounced oscillations in the delay-dependent kinetic energy release spectra were observed. The occurrence of vibrational revivals permits us to identify the potential curves of the O 2 dication which are most relevant to the molecular dynamics. These studies show the accessibility to the dynamics of such higher-charged molecules.

  6. Molecular imaging of rheumatoid arthritis by radiolabelled monoclonal antibodies: new imaging strategies to guide molecular therapies

    Energy Technology Data Exchange (ETDEWEB)

    Malviya, G.; Dierckx, R.A. [Department of Nuclear Medicine and Molecular Imaging, University Medical Centre Groningen, University of Groningen (Netherlands); Conti, F. [Rheumatology Unit, I Faculty of Medicine and Surgery, Sapienza University of Rome (Italy); Chianelli, M. [Department of Nuclear Medicine and Molecular Imaging, University Medical Centre Groningen, University of Groningen (Netherlands); Unit of Nuclear Medicine, Regina apostolorum Hospital, Albano, Rome (Italy); Scopinaro, F. [Nuclear Medicine Department, Sapienza University of Rome, St. Andrea Hospital, Rome (Italy); Signore, A. [Department of Nuclear Medicine and Molecular Imaging, University Medical Centre Groningen, University of Groningen (Netherlands); Nuclear Medicine Department, Sapienza University of Rome, St. Andrea Hospital, Rome (Italy)

    2010-02-15

    The closing of the last century opened a wide variety of approaches for inflammation imaging and treatment of patients with rheumatoid arthritis (RA). The introduction of biological therapies for the management of RA started a revolution in the therapeutic armamentarium with the development of several novel monoclonal antibodies (mAbs), which can be murine, chimeric, humanised and fully human antibodies. Monoclonal antibodies specifically bind to their target, which could be adhesion molecules, activation markers, antigens or receptors, to interfere with specific inflammation pathways at the molecular level, leading to immune-modulation of the underlying pathogenic process. These new generation of mAbs can also be radiolabelled by using direct or indirect method, with a variety of nuclides, depending upon the specific diagnostic application. For studying rheumatoid arthritis patients, several monoclonal antibodies and their fragments, including anti-TNF-{alpha}, anti-CD20, anti-CD3, anti-CD4 and anti-E-selectin antibody, have been radiolabelled mainly with {sup 99m}Tc or {sup 111}In. Scintigraphy with these radiolabelled antibodies may offer an exciting possibility for the study of RA patients and holds two types of information: (1) it allows better staging of the disease and diagnosis of the state of activity by early detection of inflamed joints that might be difficult to assess; (2) it might provide a possibility to perform 'evidence-based biological therapy' of arthritis with a view to assessing whether an antibody will localise in an inflamed joint before using the same unlabelled antibody therapeutically. This might prove particularly important for the selection of patients to be treated since biological therapies can be associated with severe side-effects and are considerably expensive. This article reviews the use of radiolabelled mAbs in the study of RA with particular emphasis on the use of different radiolabelled monoclonal antibodies for

  7. Molecular imaging of rheumatoid arthritis by radiolabelled monoclonal antibodies: new imaging strategies to guide molecular therapies

    International Nuclear Information System (INIS)

    Malviya, G.; Dierckx, R.A.; Conti, F.; Chianelli, M.; Scopinaro, F.; Signore, A.

    2010-01-01

    The closing of the last century opened a wide variety of approaches for inflammation imaging and treatment of patients with rheumatoid arthritis (RA). The introduction of biological therapies for the management of RA started a revolution in the therapeutic armamentarium with the development of several novel monoclonal antibodies (mAbs), which can be murine, chimeric, humanised and fully human antibodies. Monoclonal antibodies specifically bind to their target, which could be adhesion molecules, activation markers, antigens or receptors, to interfere with specific inflammation pathways at the molecular level, leading to immune-modulation of the underlying pathogenic process. These new generation of mAbs can also be radiolabelled by using direct or indirect method, with a variety of nuclides, depending upon the specific diagnostic application. For studying rheumatoid arthritis patients, several monoclonal antibodies and their fragments, including anti-TNF-α, anti-CD20, anti-CD3, anti-CD4 and anti-E-selectin antibody, have been radiolabelled mainly with 99m Tc or 111 In. Scintigraphy with these radiolabelled antibodies may offer an exciting possibility for the study of RA patients and holds two types of information: (1) it allows better staging of the disease and diagnosis of the state of activity by early detection of inflamed joints that might be difficult to assess; (2) it might provide a possibility to perform 'evidence-based biological therapy' of arthritis with a view to assessing whether an antibody will localise in an inflamed joint before using the same unlabelled antibody therapeutically. This might prove particularly important for the selection of patients to be treated since biological therapies can be associated with severe side-effects and are considerably expensive. This article reviews the use of radiolabelled mAbs in the study of RA with particular emphasis on the use of different radiolabelled monoclonal antibodies for therapy decision-making and

  8. MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

    Directory of Open Access Journals (Sweden)

    Paolo Ruggerone

    2013-02-01

    Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  9. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    Directory of Open Access Journals (Sweden)

    Paolo Ruggerone

    2013-02-01

    Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  10. Molecular dynamics of TBP and DBP studied by neutron transmission

    International Nuclear Information System (INIS)

    Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.

    1984-04-01

    Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt

  11. Bench to bedside molecular functional imaging in translational cancer medicine: to image or to imagine?

    International Nuclear Information System (INIS)

    Mahajan, A.; Goh, V.; Basu, S.; Vaish, R.; Weeks, A.J.; Thakur, M.H.; Cook, G.J.

    2015-01-01

    Ongoing research on malignant and normal cell biology has substantially enhanced the understanding of the biology of cancer and carcinogenesis. This has led to the development of methods to image the evolution of cancer, target specific biological molecules, and study the anti-tumour effects of novel therapeutic agents. At the same time, there has been a paradigm shift in the field of oncological imaging from purely structural or functional imaging to combined multimodal structure–function approaches that enable the assessment of malignancy from all aspects (including molecular and functional level) in a single examination. The evolving molecular functional imaging using specific molecular targets (especially with combined positron-emission tomography [PET] computed tomography [CT] using 2- [ 18 F]-fluoro-2-deoxy-D-glucose [FDG] and other novel PET tracers) has great potential in translational research, giving specific quantitative information with regard to tumour activity, and has been of pivotal importance in diagnoses and therapy tailoring. Furthermore, molecular functional imaging has taken a key place in the present era of translational cancer research, producing an important tool to study and evolve newer receptor-targeted therapies, gene therapies, and in cancer stem cell research, which could form the basis to translate these agents into clinical practice, popularly termed “theranostics”. Targeted molecular imaging needs to be developed in close association with biotechnology, information technology, and basic translational scientists for its best utility. This article reviews the current role of molecular functional imaging as one of the main pillars of translational research. -- Highlights: •Molecular functional imaging (MFI) gives insight into the tumor biology and intratumoral heterogeneity. •It has potential role in identifying radiomic signatures associated with underlying gene-expression. •Radiomics can be used to create a road map

  12. Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study

    National Research Council Canada - National Science Library

    Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy

    2006-01-01

    .... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...

  13. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  14. Proceedings of II Molecular Imaging Symposium Cuba - Japan

    International Nuclear Information System (INIS)

    2016-01-01

    In the Central Theater, University Hospital 'General Calixto Garcia' took place the II Symposium on Molecular Imaging Cuba Japan in the framework of the Scientific Convention for the 120th anniversary of the hospital. The event was organized by the hospital itself with the support of the Society of Medical Physics (medical physics section), CEADEN, the Embassy of Japan and the Theragnostic Compounds R&D Center Neuroscience Research Institute Gachon University, Incheon Korea. It was attended by 80 national scientific leaders and with the invaluable presence of Dr. Tatsuo IDO, Emeritus professor of Tohoku University (Sendai, Japan) who presented the results of the scientific papers presented this year in national and international events , referring to the new technologies of molecular imaging and the importance of medical physics in its development. During the meeting the importance of the new technologies of molecular imaging, its undisputed diagnosis intake and medical treatment and the value of human capital struggled to deal with the new technologies, the view that these are only used best when it is understood that they are multidisciplinary systems where each specialist and technical personnel plays an indispensable role. The challenge has medical physics to address these new technologies and the need for changes in the theoretical and practical training in the specialty. These analyzes will be given continuity in the next symposia molecular imaging. (author)

  15. Molecular imaging of tumor blood vessels in prostate cancer.

    Science.gov (United States)

    Tilki, Derya; Seitz, Michael; Singer, Bernhard B; Irmak, Ster; Stief, Christian G; Reich, Oliver; Ergün, Süleyman

    2009-05-01

    In the past three decades many efforts have been undertaken to understand the mechanisms of tumor angiogenesis. The introduction of anti-angiogenic drugs in tumor therapy during the last few years necessitates the establishment of new techniques enabling molecular imaging of tumor vascular remodelling. The determination of tumor size as commonly used is not appropriate since the extended necrosis under anti-angiogenic therapy does not necessarily result in the reduction of tumor diameter. The basis for the molecular imaging of tumor blood vessels is the remodelling of the tumor vessels under anti-angiogenic therapy which obviously occurs at an early stage and seems to be a convincing parameter. Beside the enormous progress in this field during the last few years the resolution is still not high enough to evaluate the remodelling of the micro tumor vessels. New imaging approaches combining specific molecular markers for tumor vessels with the different imaging techniques are needed to overcome this issue as exemplarily discussed for prostate cancer in this review. Molecular contrast agents targeting the vasculature will allow clinicians the visualization of vascular remodelling processes taking place under anti-angiogenic therapy and improve tumor diagnosis and follow-up.

  16. Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

  17. PET-MRI: the likely future of molecular imaging

    International Nuclear Information System (INIS)

    Chen Xiang; Zhao Jinhua; Zhao Jun

    2008-01-01

    PET-CT is a successful combination of functional and morphologic information, and it has already been shown to have great value both in clinics and in scientific research. MRI is another kind of morphologic imaging method, in contrast to CT, MRI can yield images with higher soft-tissue contrast and better spatial resolution. The combination of PET and MRI for simultaneous data acquisition should have far- reaching consequences for molecular imaging. This review will talk about the problems met in the development of PET-MRI and describe the progress to date and look forward to its potential application. (authors)

  18. Molecular Imaging and Precision Medicine in Uterine and Ovarian Cancers.

    Science.gov (United States)

    Zukotynski, Katherine A; Kim, Chun K

    2017-10-01

    Gynecologic cancer is a heterogeneous group of diseases both functionally and morphologically. Today, PET coupled with computed tomography (PET/CT) or PET/MR imaging play a central role in the precision medicine algorithm of patients with gynecologic malignancy. In particular, PET/CT and PET/MR imaging are molecular imaging techniques that not only are useful tools for initial staging and restaging but provide anatomofunctional insight and can serve as predictive and prognostic biomarkers of response in patients with gynecologic malignancy. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Molecular Imaging and Precision Medicine in Breast Cancer.

    Science.gov (United States)

    Chudgar, Amy V; Mankoff, David A

    2017-01-01

    Precision medicine, basing treatment approaches on patient traits and specific molecular features of disease processes, has an important role in the management of patients with breast cancer as targeted therapies continue to improve. PET imaging offers noninvasive information that is complementary to traditional tissue biomarkers, including information about tumor burden, tumor metabolism, receptor status, and proliferation. Several PET agents that image breast cancer receptors can visually demonstrate the extent and heterogeneity of receptor-positive disease and help predict which tumors are likely to respond to targeted treatments. This review presents applications of PET imaging in the targeted treatment of breast cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  1. Microscopic study of nuclear 'pasta' by quantum molecular dynamics

    International Nuclear Information System (INIS)

    Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

    2002-01-01

    Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc. and be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape. We also observe intermediate phases, which has complicated nuclear shapes. Geometrical structures of matter are analyzed with Minkowski functionals, and it is found out that intermediate phases can be characterized as ones with negative Euler characteristic. Our result suggests the existence of these kinds of phases in addition to the simple 'pasta' phases in neutron star crusts. (author)

  2. Nonlinear dynamics of zigzag molecular chains (in Russian)

    DEFF Research Database (Denmark)

    Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth

    1999-01-01

    models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...

  3. The chaos and order in nuclear molecular dynamics

    International Nuclear Information System (INIS)

    Srokowski, T.

    1995-01-01

    The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs

  4. Molecular Imaging of the ATM Kinase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Terence M. [Department of Radiation Oncology, Ohio State University, Columbus, Ohio (United States); Nyati, Shyam [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Center for Molecular Imaging, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Ross, Brian D. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Department of Radiology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Rehemtulla, Alnawaz, E-mail: alnawaz@umich.edu [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Center for Molecular Imaging, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Department of Radiology, University of Michigan Medical Center, Ann Arbor, Michigan (United States)

    2013-08-01

    Purpose: Ataxia telangiectasia mutated (ATM) is a serine/threonine kinase critical to the cellular DNA-damage response, including from DNA double-strand breaks. ATM activation results in the initiation of a complex cascade of events including DNA damage repair, cell cycle checkpoint control, and survival. We sought to create a bioluminescent reporter that dynamically and noninvasively measures ATM kinase activity in living cells and subjects. Methods and Materials: Using the split luciferase technology, we constructed a hybrid cDNA, ATM-reporter (ATMR), coding for a protein that quantitatively reports on changes in ATM kinase activity through changes in bioluminescence. Results: Treatment of ATMR-expressing cells with ATM inhibitors resulted in a dose-dependent increase in bioluminescence activity. In contrast, induction of ATM kinase activity upon irradiation resulted in a decrease in reporter activity that correlated with ATM and Chk2 activation by immunoblotting in a time-dependent fashion. Nuclear targeting improved ATMR sensitivity to both ATM inhibitors and radiation, whereas a mutant ATMR (lacking the target phosphorylation site) displayed a muted response. Treatment with ATM inhibitors and small interfering (si)RNA-targeted knockdown of ATM confirm the specificity of the reporter. Using reporter expressing xenografted tumors demonstrated the ability of ATMR to report in ATM activity in mouse models that correlated in a time-dependent fashion with changes in Chk2 activity. Conclusions: We describe the development and validation of a novel, specific, noninvasive bioluminescent reporter that enables monitoring of ATM activity in real time, in vitro and in vivo. Potential applications of this reporter include the identification and development of novel ATM inhibitors or ATM-interacting partners through high-throughput screens and in vivo pharmacokinetic/pharmacodynamic studies of ATM inhibitors in preclinical models.

  5. Molecular subtypes and imaging phenotypes of breast cancer

    International Nuclear Information System (INIS)

    Cho, Nariya

    2016-01-01

    During the last 15 years, traditional breast cancer classifications based on histopathology have been reorganized into the luminal A, luminal B, human epidermal growth factor receptor 2 (HER2), and basal-like subtypes based on gene expression profiling. Each molecular subtype has shown varying risk for progression, response to treatment, and survival outcomes. Research linking the imaging phenotype with the molecular subtype has revealed that non-calcified, relatively circumscribed masses with posterior acoustic enhancement are common in the basal-like subtype, spiculated masses with a poorly circumscribed margin and posterior acoustic shadowing in the luminal subtype, and pleomorphic calcifications in the HER2-enriched subtype. Understanding the clinical implications of the molecular subtypes and imaging phenotypes could help radiologists guide precision medicine, tailoring medical treatment to patients and their tumor characteristics

  6. Molecular subtypes and imaging phenotypes of breast cancer

    Directory of Open Access Journals (Sweden)

    Nariya Cho

    2016-10-01

    Full Text Available During the last 15 years, traditional breast cancer classifications based on histopathology have been reorganized into the luminal A, luminal B, human epidermal growth factor receptor 2 (HER2, and basal-like subtypes based on gene expression profiling. Each molecular subtype has shown varying risk for progression, response to treatment, and survival outcomes. Research linking the imaging phenotype with the molecular subtype has revealed that non-calcified, relatively circumscribed masses with posterior acoustic enhancement are common in the basal-like subtype, spiculated masses with a poorly circumscribed margin and posterior acoustic shadowing in the luminal subtype, and pleomorphic calcifications in the HER2-enriched subtype. Understanding the clinical implications of the molecular subtypes and imaging phenotypes could help radiologists guide precision medicine, tailoring medical treatment to patients and their tumor characteristics.

  7. Molecular subtypes and imaging phenotypes of breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Nariya [Dept. of Radiology, Seoul National University Hospital, Seoul (Korea, Republic of)

    2016-08-15

    During the last 15 years, traditional breast cancer classifications based on histopathology have been reorganized into the luminal A, luminal B, human epidermal growth factor receptor 2 (HER2), and basal-like subtypes based on gene expression profiling. Each molecular subtype has shown varying risk for progression, response to treatment, and survival outcomes. Research linking the imaging phenotype with the molecular subtype has revealed that non-calcified, relatively circumscribed masses with posterior acoustic enhancement are common in the basal-like subtype, spiculated masses with a poorly circumscribed margin and posterior acoustic shadowing in the luminal subtype, and pleomorphic calcifications in the HER2-enriched subtype. Understanding the clinical implications of the molecular subtypes and imaging phenotypes could help radiologists guide precision medicine, tailoring medical treatment to patients and their tumor characteristics.

  8. Molecular Ultrasound Imaging for the Detection of Neural Inflammation

    Science.gov (United States)

    Volz, Kevin R.

    Molecular imaging is a form of nanotechnology that enables the noninvasive examination of biological processes in vivo. Radiopharmaceutical agents are used to selectively target biochemical markers, which permits their detection and evaluation. Early visualization of molecular variations indicative of pathophysiological processes can aid in patient diagnoses and management decisions. Molecular imaging is performed by introducing molecular probes into the body. Molecular probes are often contrast agents that have been nanoengineered to selectively target and tether to molecules, enabling their radiologic identification. Ultrasound contrast agents have been demonstrated as an effective method of detecting perfusion at the tissue level. Through a nanoengineering process, ultrasound contrast agents can be targeted to specific molecules, thereby extending ultrasound's capabilities from the tissue to molecular level. Molecular ultrasound, or targeted contrast enhanced ultrasound (TCEUS), has recently emerged as a popular molecular imaging technique due to its ability to provide real-time anatomical and functional information in the absence of ionizing radiation. However, molecular ultrasound represents a novel form of molecular imaging, and consequently remains largely preclinical. A review of the TCEUS literature revealed multiple preclinical studies demonstrating its success in detecting inflammation in a variety of tissues. Although, a gap was identified in the existing evidence, as TCEUS effectiveness for detection of neural inflammation in the spinal cord was unable to be uncovered. This gap in knowledge, coupled with the profound impacts that this TCEUS application could have clinically, provided rationale for its exploration, and use as contributory evidence for the molecular ultrasound body of literature. An animal model that underwent a contusive spinal cord injury was used to establish preclinical evidence of TCEUS to detect neural inflammation. Imaging was

  9. Image Alignment for Multiple Camera High Dynamic Range Microscopy

    OpenAIRE

    Eastwood, Brian S.; Childs, Elisabeth C.

    2012-01-01

    This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability fo...

  10. Statistical ensembles and molecular dynamics studies of anisotropic solids. II

    International Nuclear Information System (INIS)

    Ray, J.R.; Rahman, A.

    1985-01-01

    We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities

  11. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

  12. Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)

    2007-02-14

    We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 A. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

  13. Fermionic molecular dynamics for ground states and collisions of nuclei

    International Nuclear Information System (INIS)

    Feldmeier, H.; Bieler, K.; Schnack, J.

    1994-08-01

    The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)

  14. Fermionic molecular dynamics for colliding and decaying nuclei

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    1993-11-01

    Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

  15. Optical spectra and lattice dynamics of molecular crystals

    CERN Document Server

    Zhizhin, GN

    1995-01-01

    The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

  16. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Christian Mücksch

    Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

  17. Stereochemical errors and their implications for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Freddolino Peter L

    2011-05-01

    Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

  18. Ultrafast dissociation: An unexpected tool for probing molecular dynamics

    International Nuclear Information System (INIS)

    Morin, Paul; Miron, Catalin

    2012-01-01

    Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

  19. Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

    KAUST Repository

    Yoon, Seyoon; Monteiro, Paulo J.M.

    2013-01-01

    The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

  20. Optical imaging of tumor hypoxia dynamics

    Science.gov (United States)

    Palmer, Gregory M.; Fontanella, Andrew N.; Zhang, Guoqing; Hanna, Gabi; Fraser, Cassandra L.; Dewhirst, Mark W.

    2010-11-01

    The influence of the tumor microenvironment and hypoxia plays a significant role in determining cancer progression, treatment response, and treatment resistance. That the tumor microenvironment is highly heterogeneous with significant intratumor and intertumor variability presents a significant challenge in developing effective cancer therapies. Critical to understanding the role of the tumor microenvironment is the ability to dynamically quantify oxygen levels in the vasculature and tissue in order to elucidate the roles of oxygen supply and consumption, spatially and temporally. To this end, we describe the use of hyperspectral imaging to characterize hemoglobin absorption to quantify hemoglobin content and oxygen saturation, as well as dual emissive fluorescent/phosphorescent boron nanoparticles, which serve as ratiometric indicators of tissue oxygen tension. Applying these techniques to a window-chamber tumor model illustrates the role of fluctuations in hemoglobin saturation in driving changes in tissue oxygenation, the two being significantly correlated (r = 0.77). Finally, a green-fluorescence-protein reporter for hypoxia inducible factor-1 (HIF-1) provides an endpoint for hypoxic stress in the tumor, which is used to demonstrate a significant association between tumor hypoxia dynamics and HIF-1 activity in an in vivo demonstration of the technique.

  1. Dynamic imaging with coincidence gamma camera

    International Nuclear Information System (INIS)

    Elhmassi, Ahmed

    2008-01-01

    In this paper we develop a technique to calculate dynamic parameters from data acquired using gamma-camera PET (gc PET). Our method is based on an algorithm development for dynamic SPECT, which processes all decency projection data simultaneously instead of reconstructing a series of static images individually. The algorithm was modified to account for the extra data that is obtained with gc PET (compared with SPEC). The method was tested using simulated projection data for both a SPECT and a gc PET geometry. These studies showed the ability of the code to reconstruct simulated data with a varying range of half-lives. The accuracy of the algorithm was measured in terms of the reconstructed half-life and initial activity for the simulated object. The reconstruction of gc PET data showed improvement in half-life and activity compared to SPECT data of 23% and 20%, respectively (at 50 iterations). The gc PET algorithm was also tested using data from an experimental phantom and finally, applied to a clinical dataset, where the algorithm was further modified to deal with the situation where the activity in certain pixels decreases and then increases during the acquisition. (author)

  2. Current Molecular Imaging Positron Emitting Radiotracers in Oncology

    International Nuclear Information System (INIS)

    Zhu, Aizhi; Shim, Hyunsuk

    2011-01-01

    Molecular imaging is one of the fastest growing areas of medical imaging. Positron emission tomography has been widely used in the clinical management of patients with cancer. Nuclear imaging provides biological information at the cellular, subcellular, and molecular level in living subjects with noninvasive procedures. In particular, PET imaging takes advantage of traditional diagnostic imaging techniques and introduces positron emitting probes to determine the expression of indicative molecular targets at different stages of cancer. 18F fluorodeoxyglucose ( 18F FDG), the only FDA approved oncological PET tracer, has been widely utilized in cancer diagnosis, staging, restaging, and even monitoring response to therapy; however, 18F FDG is not a tumor specific PET tracer. Over the last decade, many promising tumor specific PET tracer. Over the last decade, many promising tumor specific PET tracers have been developed and evaluated in preclinical and clinical studies. This review provides an overview of the current non 18F FDG PET tracers in oncology that have been developed based on tumor characteristics such as increased metabolism, hyperproliferation, angiogenesis, hypoxia, apoptosis, and tumor specific antigens and surface receptors

  3. Exogenous Molecular Probes for Targeted Imaging in Cancer: Focus on Multi-modal Imaging

    International Nuclear Information System (INIS)

    Joshi, Bishnu P.; Wang, Thomas D.

    2010-01-01

    Cancer is one of the major causes of mortality and morbidity in our healthcare system. Molecular imaging is an emerging methodology for the early detection of cancer, guidance of therapy, and monitoring of response. The development of new instruments and exogenous molecular probes that can be labeled for multi-modality imaging is critical to this process. Today, molecular imaging is at a crossroad, and new targeted imaging agents are expected to broadly expand our ability to detect and manage cancer. This integrated imaging strategy will permit clinicians to not only localize lesions within the body but also to manage their therapy by visualizing the expression and activity of specific molecules. This information is expected to have a major impact on drug development and understanding of basic cancer biology. At this time, a number of molecular probes have been developed by conjugating various labels to affinity ligands for targeting in different imaging modalities. This review will describe the current status of exogenous molecular probes for optical, scintigraphic, MRI and ultrasound imaging platforms. Furthermore, we will also shed light on how these techniques can be used synergistically in multi-modal platforms and how these techniques are being employed in current research

  4. High-temperature annealing of graphite: A molecular dynamics study

    Science.gov (United States)

    Petersen, Andrew; Gillette, Victor

    2018-05-01

    A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

  5. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  6. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  7. Incorporation of quantum statistical features in molecular dynamics

    International Nuclear Information System (INIS)

    Ohnishi, Akira; Randrup, J.

    1995-01-01

    We formulate a method for incorporating quantum fluctuations into molecular-dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum-statistical equilibrium. (author)

  8. Molecular Dynamics Simulations of Tensile Behavior of Copper

    OpenAIRE

    Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.

    2014-01-01

    Molecular dynamics simulations on tensile deformation of initially defect free single crystal copper nanowire oriented in {100} has been carried out at 10 K under adiabatic and isothermal loading conditions. The tensile behaviour was characterized by sharp rise in stress in elastic regime followed by sudden drop at the point of dislocation nucleation. The important finding is that the variation in dislocation density is correlated with the observed stress-strain response. Several interesting ...

  9. Automated processing of data generated by molecular dynamics

    International Nuclear Information System (INIS)

    Lobato Hoyos, Ivan; Rojas Tapia, Justo; Instituto Peruano de Energia Nuclear, Lima

    2008-01-01

    A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)

  10. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane

    OpenAIRE

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-01-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...

  11. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    International Nuclear Information System (INIS)

    Swygenhoven, H. van; Caro, A.

    1997-01-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young's modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs

  12. Accelerating Molecular Dynamic Simulation on Graphics Processing Units

    Science.gov (United States)

    Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.

    2009-01-01

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337

  13. Molecular dynamics simulation of cascade damage in gold

    International Nuclear Information System (INIS)

    Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.

    1997-01-01

    High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists

  14. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    Wang Hanfu; Chu Weiguo

    2009-01-01

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  15. Fragmentation dynamics of molecular hydrogen in strong ultrashort laser pulses

    International Nuclear Information System (INIS)

    Rudenko, A; Feuerstein, B; Zrost, K; Jesus, V L B de; Ergler, T; Dimopoulou, C; Schroeter, C D; Moshammer, R; Ullrich, J

    2005-01-01

    We present the results of a systematic experimental study of dissociation and Coulomb explosion of molecular hydrogen induced by intense ultrashort (7-25 fs) laser pulses. Using coincident recoil-ion momentum spectroscopy we can distinguish the contributions from dissociation and double ionization even if they result in the same kinetic energies of the fragments. The dynamics of all fragmentation channels drastically depends on the pulse duration, and for 7 fs pulses becomes extremely sensitive to the pulse shape

  16. Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

    2007-01-01

    The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

  17. Molecular dynamics simulation of bubble nucleation in explosive boiling

    International Nuclear Information System (INIS)

    Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang

    2009-01-01

    Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)

  18. Shapiro like steps reveals molecular nanomagnets’ spin dynamics

    International Nuclear Information System (INIS)

    Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

    2015-01-01

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

  19. Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2017-07-01

    Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.

  20. PET molecular imaging in stem cell therapy for neurological diseases

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jiachuan; Zhang, Hong [Second Affiliated Hospital of Zhejiang University School of Medicine, Department of Nuclear Medicine, Hangzhou, Zhejiang (China); Zhejiang University, Medical PET Center, Hangzhou (China); Institute of Nuclear Medicine and Molecular Imaging of Zhejiang University, Hangzhou (China); Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou (China); Tian, Mei [University of Texas, M.D. Anderson Cancer Center, Department of Experimental Diagnostic Imaging, Houston, TX (United States)

    2011-10-15

    Human neurological diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, spinal cord injury and multiple sclerosis are caused by loss of different types of neurons and glial cells in the brain and spinal cord. At present, there are no effective therapies against these disorders. Discovery of the therapeutic potential of stem cells offers new strategies for the treatment of neurological diseases. Direct assessment of stem cells' survival, interaction with the host and impact on neuronal functions after transplantation requires advanced in vivo imaging techniques. Positron emission tomography (PET) is a potential molecular imaging modality to evaluate the viability and function of transplanted tissue or stem cells in the nervous system. This review focuses on PET molecular imaging in stem cell therapy for neurological diseases. (orig.)

  1. Molecular Imaging of Apoptosis: From Micro to Macro

    Science.gov (United States)

    Zeng, Wenbin; Wang, Xiaobo; Xu, Pengfei; Liu, Gang; Eden, Henry S.; Chen, Xiaoyuan

    2015-01-01

    Apoptosis, or programmed cell death, is involved in numerous human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer, and is often confused with other types of cell death. Therefore strategies that enable visualized detection of apoptosis would be of enormous benefit in the clinic for diagnosis, patient management, and development of new therapies. In recent years, improved understanding of the apoptotic machinery and progress in imaging modalities have provided opportunities for researchers to formulate microscopic and macroscopic imaging strategies based on well-defined molecular markers and/or physiological features. Correspondingly, a large collection of apoptosis imaging probes and approaches have been documented in preclinical and clinical studies. In this review, we mainly discuss microscopic imaging assays and macroscopic imaging probes, ranging in complexity from simple attachments of reporter moieties to proteins that interact with apoptotic biomarkers, to rationally designed probes that target biochemical changes. Their clinical translation will also be our focus. PMID:25825597

  2. Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kim, Woongkee; Kaviany, Massoud; Shim, J. H.

    2014-01-01

    It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments

  3. Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets

    Science.gov (United States)

    Lehmann, Kevin K.

    2003-03-01

    Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.

  4. Excitation dynamics and relaxation in a molecular heterodimer

    International Nuclear Information System (INIS)

    Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

    2012-01-01

    Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

  5. Molecular dynamics simulations of solutions at constant chemical potential

    Science.gov (United States)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  6. Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

    Energy Technology Data Exchange (ETDEWEB)

    Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

    2017-04-04

    The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

  7. Electron-nuclear corellations for photoinduced dynamics in molecular dimers

    Science.gov (United States)

    Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

    2003-03-01

    Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

  8. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

    NARCIS (Netherlands)

    van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  9. A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

    NARCIS (Netherlands)

    van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  10. In vivo molecular and genomic imaging: new challenges for imaging physics.

    Science.gov (United States)

    Cherry, Simon R

    2004-02-07

    The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.

  11. In vivo molecular and genomic imaging: new challenges for imaging physics

    Energy Technology Data Exchange (ETDEWEB)

    Cherry, Simon R [Department of Biomedical Engineering, University of California, Davis, CA (United States)

    2004-02-07

    The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field. (topical review)

  12. In vivo molecular and genomic imaging: new challenges for imaging physics

    International Nuclear Information System (INIS)

    Cherry, Simon R

    2004-01-01

    The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field. (topical review)

  13. Multi-modality molecular imaging: pre-clinical laboratory configuration

    Science.gov (United States)

    Wu, Yanjun; Wellen, Jeremy W.; Sarkar, Susanta K.

    2006-02-01

    In recent years, the prevalence of in vivo molecular imaging applications has rapidly increased. Here we report on the construction of a multi-modality imaging facility in a pharmaceutical setting that is expected to further advance existing capabilities for in vivo imaging of drug distribution and the interaction with their target. The imaging instrumentation in our facility includes a microPET scanner, a four wavelength time-domain optical imaging scanner, a 9.4T/30cm MRI scanner and a SPECT/X-ray CT scanner. An electronics shop and a computer room dedicated to image analysis are additional features of the facility. The layout of the facility was designed with a central animal preparation room surrounded by separate laboratory rooms for each of the major imaging modalities to accommodate the work-flow of simultaneous in vivo imaging experiments. This report will focus on the design of and anticipated applications for our microPET and optical imaging laboratory spaces. Additionally, we will discuss efforts to maximize the daily throughput of animal scans through development of efficient experimental work-flows and the use of multiple animals in a single scanning session.

  14. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  15. Dynamic imaging through turbid media based on digital holography.

    Science.gov (United States)

    Li, Shiping; Zhong, Jingang

    2014-03-01

    Imaging through turbid media using visible or IR light instead of harmful x ray is still a challenging problem, especially in dynamic imaging. A method of dynamic imaging through turbid media using digital holography is presented. In order to match the coherence length between the dynamic object wave and the reference wave, a cw laser is used. To solve the problem of difficult focusing in imaging through turbid media, an autofocus technology is applied. To further enhance the image contrast, a spatial filtering technique is used. A description of digital holography and experiments of imaging the objects hidden in turbid media are presented. The experimental result shows that dynamic images of the objects can be achieved by the use of digital holography.

  16. Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

    Science.gov (United States)

    Hu, Hao; Liu, Haiyan

    2013-05-30

    Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

  17. Molecular imaging of brown adipose tissue in health and disease

    International Nuclear Information System (INIS)

    Bauwens, Matthias; Wierts, Roel; Brans, Boudewijn; Royen, Bart van; Backes, Walter; Bucerius, Jan; Mottaghy, Felix

    2014-01-01

    Brown adipose tissue (BAT) has transformed from an interfering tissue in oncological 18 F-fluorodeoxyglucose (FDG) positron emission tomography (PET) to an independent imaging research field. This review takes the perspective from the imaging methodology on which human BAT research has come to rely on heavily. This review analyses relevant PubMed-indexed publications that discuss molecular imaging methods of BAT. In addition, reported links between BAT and human diseases such as obesity are discussed, and the possibilities for imaging in these fields are highlighted. Radiopharmaceuticals aiming at several different biological mechanisms of BAT are discussed and evaluated. Prospective, dedicated studies allow visualization of BAT function in a high percentage of human subjects. BAT dysfunction has been implicated in obesity, linked with diabetes and associated with cachexia and atherosclerosis. Presently, 18 F-FDG PET/CT is the most useful tool for evaluating therapies aiming at BAT activity. In addition to 18 F-FDG, other radiopharmaceuticals such as 99m Tc-sestamibi, 123 I-metaiodobenzylguanidine (MIBG), 18 F-fluorodopa and 18 F-14(R,S)-[ 18 F]fluoro-6-thia-heptadecanoic acid (FTHA) may have a potential for visualizing other aspects of BAT activity. MRI methods are under continuous development and provide the prospect of functional imaging without ionizing radiation. Molecular imaging of BAT can be used to quantitatively assess different aspects of BAT metabolic activity. (orig.)

  18. Molecular imaging of brown adipose tissue in health and disease

    Energy Technology Data Exchange (ETDEWEB)

    Bauwens, Matthias [MUMC, Department of Medical Imaging, Division of Nuclear Medicine, Maastricht (Netherlands); Maastricht University, Research School NUTRIM, Maastricht (Netherlands); Wierts, Roel; Brans, Boudewijn [MUMC, Department of Medical Imaging, Division of Nuclear Medicine, Maastricht (Netherlands); Royen, Bart van; Backes, Walter [MUMC, Department of Medical Imaging, Division of Radiology, Maastricht (Netherlands); Bucerius, Jan [MUMC, Department of Medical Imaging, Division of Nuclear Medicine, Maastricht (Netherlands); Uniklinikum Aachen, Division of Nuclear Medicine, Aachen (Germany); Maastricht University, Research School CARIM, Maastricht (Netherlands); Mottaghy, Felix [MUMC, Department of Medical Imaging, Division of Nuclear Medicine, Maastricht (Netherlands); Uniklinikum Aachen, Division of Nuclear Medicine, Aachen (Germany)

    2014-04-15

    Brown adipose tissue (BAT) has transformed from an interfering tissue in oncological {sup 18}F-fluorodeoxyglucose (FDG) positron emission tomography (PET) to an independent imaging research field. This review takes the perspective from the imaging methodology on which human BAT research has come to rely on heavily. This review analyses relevant PubMed-indexed publications that discuss molecular imaging methods of BAT. In addition, reported links between BAT and human diseases such as obesity are discussed, and the possibilities for imaging in these fields are highlighted. Radiopharmaceuticals aiming at several different biological mechanisms of BAT are discussed and evaluated. Prospective, dedicated studies allow visualization of BAT function in a high percentage of human subjects. BAT dysfunction has been implicated in obesity, linked with diabetes and associated with cachexia and atherosclerosis. Presently, {sup 18}F-FDG PET/CT is the most useful tool for evaluating therapies aiming at BAT activity. In addition to {sup 18}F-FDG, other radiopharmaceuticals such as {sup 99m}Tc-sestamibi, {sup 123}I-metaiodobenzylguanidine (MIBG), {sup 18}F-fluorodopa and {sup 18}F-14(R,S)-[{sup 18}F]fluoro-6-thia-heptadecanoic acid (FTHA) may have a potential for visualizing other aspects of BAT activity. MRI methods are under continuous development and provide the prospect of functional imaging without ionizing radiation. Molecular imaging of BAT can be used to quantitatively assess different aspects of BAT metabolic activity. (orig.)

  19. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  20. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

    Ould-Kaddour, F.; Barrat, J.L.

    1991-05-01

    Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

  1. Molecular dynamics of coalescence and collisions of silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Guevara-Chapa, Enrique, E-mail: enrique_guevara@hotmail.com [Universidad Autónoma de Nuevo León, Facultad de Ciencias Físico Matemáticas (Mexico); Mejía-Rosales, Sergio [Universidad Autónoma de Nuevo León, Center for Innovation, Research and Development in Engineering and Technology (CIIDIT), and CICFIM-Facultad de Ciencias Físico Matemáticas (Mexico)

    2014-12-15

    We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy.

  2. Molecular dynamics simulations of lysozyme in water/sugar solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2008-04-18

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  3. Molecular dynamics of coalescence and collisions of silver nanoparticles

    International Nuclear Information System (INIS)

    Guevara-Chapa, Enrique; Mejía-Rosales, Sergio

    2014-01-01

    We study how different relative orientations and impact velocity on the collision of two silver nanoparticles affect the first stages of the formation of a new, larger nanoparticle. In order to do this, we implemented a set of molecular dynamics simulations on the NVE ensemble on pairs of silver icosahedral nanoparticles at several relative orientations, that allowed us to follow the dynamics of the first nanoseconds of the coalescence processes. Using bond angle analysis, we found that the initial relative orientation of the twin planes has a critical role on the final stability of the resulting particle, and on the details of the dynamics itself. When the original particles have their closest twins aligned to each other, the formed nanoparticle will likely stabilize its structure onto a particle with a defined center and a low surface-to-volume ratio, while nanoparticles with misaligned twins will promote the formation of highly defective particles with a high inner energy

  4. Liquid-vapor coexistence by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Baranyai, Andras; Cummings, Peter T.

    2000-01-01

    We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics

  5. The classical and quantum dynamics of molecular spins on graphene

    Science.gov (United States)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2016-02-01

    Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

  6. Progress in Molecular Imaging in Endoscopy and Endomicroscopy for Cancer Imaging

    Directory of Open Access Journals (Sweden)

    Supang Khondee

    2013-01-01

    Full Text Available Imaging is an essential tool for effective cancer management. Endoscopes are important medical instruments for performing in vivo imaging in hollow organs. Early detection of cancer can be achieved with surveillance using endoscopy, and has been shown to reduce mortality and to improve outcomes. Recently, great advancements have been made in endoscopic instruments, including new developments in optical designs, light sources, optical fibers, miniature scanners, and multimodal systems, allowing for improved resolution, greater tissue penetration, and multispectral imaging. In addition, progress has been made in the development of highly-specific optical probes, allowing for improved specificity for molecular targets. Integration of these new endoscopic instruments with molecular probes provides a unique opportunity for significantly improving patient outcomes and has potential to further improve early detection, image guided therapy, targeted therapy, and personalized medicine. This work summarizes current and evolving endoscopic technologies, and provides an overview of various promising optical molecular probes.

  7. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

    Directory of Open Access Journals (Sweden)

    Jinxiang Xi

    2018-03-01

    Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of

  8. Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

    Science.gov (United States)

    Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

    2018-03-27

    Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high

  9. Machine learning molecular dynamics for the simulation of infrared spectra.

    Science.gov (United States)

    Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

    2017-10-01

    Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

  10. Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

    Directory of Open Access Journals (Sweden)

    Elena ePapaleo

    2015-05-01

    Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  11. Accelerated molecular dynamics methods: introduction and recent developments

    International Nuclear Information System (INIS)

    Uberuaga, Blas Pedro; Voter, Arthur F.; Perez, Danny; Shim, Y.; Amar, J.G.

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) (10, 19, 23) to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what

  12. Accelerated molecular dynamics methods: introduction and recent developments

    Energy Technology Data Exchange (ETDEWEB)

    Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what

  13. Imaging modes of atomic force microscopy for application in molecular and cell biology.

    Science.gov (United States)

    Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

    2017-04-06

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  14. Molecular Imaging Probes for Positron Emission Tomography and Optical Imaging of Sentinel Lymph Node and Tumor

    Science.gov (United States)

    Qin, Zhengtao

    Molecular imaging is visualizations and measurements of in vivo biological processes at the molecular or cellular level using specific imaging probes. As an emerging technology, biocompatible macromolecular or nanoparticle based targeted imaging probes have gained increasing popularities. Those complexes consist of a carrier, an imaging reporter, and a targeting ligand. The active targeting ability dramatically increases the specificity. And the multivalency effect may further reduce the dose while providing a decent signal. In this thesis, sentinel lymph node (SLN) mapping and cancer imaging are two research topics. The focus is to develop molecular imaging probes with high specificity and sensitivity, for Positron Emission Tomography (PET) and optical imaging. The objective of this thesis is to explore dextran radiopharmaceuticals and porous silicon nanoparticles based molecular imaging agents. Dextran polymers are excellent carriers to deliver imaging reporters or therapeutic agents due to its well established safety profile and oligosaccharide conjugation chemistry. There is also a wide selection of dextran polymers with different lengths. On the other hand, Silicon nanoparticles represent another class of biodegradable materials for imaging and drug delivery. The success in fluorescence lifetime imaging and enhancements of the immune activation potency was briefly discussed. Chapter 1 begins with an overview on current molecular imaging techniques and imaging probes. Chapter 2 presents a near-IR dye conjugated probe, IRDye 800CW-tilmanocept. Fluorophore density was optimized to generate the maximum brightness. It was labeled with 68Ga and 99mTc and in vivo SLN mapping was successfully performed in different animals, such as mice, rabbits, dogs and pigs. With 99mTc labeled IRDye 800CW-tilmanocept, chapter 3 introduces a two-day imaging protocol with a hand-held imager. Chapter 4 proposed a method to dual radiolabel the IRDye 800CW-tilmanocept with both 68Ga and

  15. Dynamic measurements of flowing cells labeled by gold nanoparticles using full-field photothermal interferometric imaging

    Science.gov (United States)

    Turko, Nir A.; Roitshtain, Darina; Blum, Omry; Kemper, Björn; Shaked, Natan T.

    2017-06-01

    We present highly dynamic photothermal interferometric phase microscopy for quantitative, selective contrast imaging of live cells during flow. Gold nanoparticles can be biofunctionalized to bind to specific cells, and stimulated for local temperature increase due to plasmon resonance, causing a rapid change of the optical phase. These phase changes can be recorded by interferometric phase microscopy and analyzed to form an image of the binding sites of the nanoparticles in the cells, gaining molecular specificity. Since the nanoparticle excitation frequency might overlap with the sample dynamics frequencies, photothermal phase imaging was performed on stationary or slowly dynamic samples. Furthermore, the computational analysis of the photothermal signals is time consuming. This makes photothermal imaging unsuitable for applications requiring dynamic imaging or real-time analysis, such as analyzing and sorting cells during fast flow. To overcome these drawbacks, we utilized an external interferometric module and developed new algorithms, based on discrete Fourier transform variants, enabling fast analysis of photothermal signals in highly dynamic live cells. Due to the self-interference module, the cells are imaged with and without excitation in video-rate, effectively increasing signal-to-noise ratio. Our approach holds potential for using photothermal cell imaging and depletion in flow cytometry.

  16. Nanotechnology-Enabled Optical Molecular Imaging of Breast Cancer

    Science.gov (United States)

    2011-07-01

    quantitatively and dynamically detect molecular markers of breast cancer in vivo without tissue removal or directly after removal in a surgical...hour oshells by c es, the nano ting to a fin ER2- positiv (CHTN) th tinction spect ter of 276 nm sert depicts co microscopy. n was visua rption...conclusively determine the penetration depth of the nanoshells. Additionally, a quantitative difference of the nanoshell signal at the surface of the Her2

  17. Optimisation in X-ray and Molecular Imaging 2015

    International Nuclear Information System (INIS)

    Baath, Magnus; Hoeschen, Christoph; Mattsson, Soeren; Mansson, Lars Gunnar

    2016-01-01

    This issue of Radiation Protection Dosimetry is based on contributions to Optimisation in X-ray and Molecular Imaging 2015 - the 4. Malmoe Conference on Medical Imaging (OXMI 2015). The conference was jointly organised by members of former and current research projects supported by the European Commission EURATOM Radiation Protection Research Programme, in cooperation with the Swedish Society for Radiation Physics. The conference brought together over 150 researchers and other professionals from hospitals, universities and industries with interests in different aspects of the optimisation of medical imaging. More than 100 presentations were given at this international gathering of medical physicists, radiologists, engineers, technicians, nurses and educational researchers. Additionally, invited talks were offered by world-renowned experts on radiation protection, spectral imaging and medical image perception, thus covering several important aspects of the generation and interpretation of medical images. The conference consisted of 13 oral sessions and a poster session, as reflected by the conference title connected by their focus on the optimisation of the use ionising radiation in medical imaging. The conference included technology-specific topics such as computed tomography and tomosynthesis, but also generic issues of interest for the optimisation of all medical imaging, such as image perception and quality assurance. Radiation protection was covered by e.g. sessions on patient dose benchmarking and occupational exposure. Technically-advanced topics such as modelling, Monte Carlo simulation, reconstruction, classification, and segmentation were seen taking advantage of recent developments of hardware and software, showing that the optimisation community is at the forefront of technology and adapts well to new requirements. These peer-reviewed proceedings, representing a continuation of a series of selected reports from meetings in the field of medical imaging

  18. Imaging complex nutrient dynamics in mycelial networks.

    Science.gov (United States)

    Fricker, M D; Lee, J A; Bebber, D P; Tlalka, M; Hynes, J; Darrah, P R; Watkinson, S C; Boddy, L

    2008-08-01

    Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier

  19. Molecular imaging and the neuropathologies of Parkinson's disease

    DEFF Research Database (Denmark)

    Cumming, Paul; Borghammer, Per

    2012-01-01

    The main motor symptoms of Parkinson's disease (PD) are linked to degeneration of the nigrostriatal dopamine (DA) fibers, especially those innervating the putamen. This degeneration can be assessed in molecular imaging studies with presynaptic tracers such as [(18)F]-fluoro-L-DOPA (FDOPA...... with denervation upregulation, but there is an accelerated rate of DA receptor loss as the disease advances. Animal studies and post mortem investigations reveal changes in brain opioid peptide systems, but these are poorly documented in imaging studies of PD. Relatively minor changes in the binding sites for GABA...

  20. Molecular Imaging and Precision Medicine in Head and Neck Cancer.

    Science.gov (United States)

    Mena, Esther; Thippsandra, Shwetha; Yanamadala, Anusha; Redy, Siddaling; Pattanayak, Puskar; Subramaniam, Rathan M

    2017-01-01

    The concept of using tumor genomic profiling information has revolutionized personalized cancer treatment. Head and neck (HN) cancer management is being influenced by recent discoveries of activating mutations in epidermal growth factor receptor and related targeted therapies with tyrosine kinase inhibitors, targeted therapies for Kristen Rat Sarcoma, and MET proto-oncogenes. Molecular imaging using PET plays an important role in assessing the biologic behavior of HN cancer with the goal of delivering individualized cancer treatment. This review summarizes recent genomic discoveries in HN cancer and their implications for functional PET imaging in assessing response to targeted therapies, and drug resistance mechanisms. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  2. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H.G.; Muckerman, J.T.

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  3. Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers

    Science.gov (United States)

    Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen

    1999-06-01

    Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.

  4. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  5. DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

    NARCIS (Netherlands)

    JUFFER, AH; BERENDSEN, HJC

    1993-01-01

    A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

  6. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations

    NARCIS (Netherlands)

    Risselada, H. Jelger; Marrink, Siewert J.

    2009-01-01

    The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high

  7. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

    NARCIS (Netherlands)

    Marrink, SJ; Mark, AE

    2003-01-01

    Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

  8. Reaction Ensemble Molecular Dynamics: Direct Simulation of the Dynamic Equilibrium Properties of Chemically Reacting Mixtures

    Czech Academy of Sciences Publication Activity Database

    Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.

    2004-01-01

    Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004

  9. Physical properties of Cu nanoparticles: A molecular dynamics study

    International Nuclear Information System (INIS)

    Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

    2014-01-01

    Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index

  10. Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

    Science.gov (United States)

    Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

    2018-04-01

    Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

  11. Functional and molecular imaging with MRI: potential applications in paediatric radiology

    International Nuclear Information System (INIS)

    Arthurs, Owen J.; Gallagher, Ferdia A.

    2011-01-01

    MRI is a very versatile tool for noninvasive imaging and it is particularly attractive as an imaging technique in paediatric patients given the absence of ionizing radiation. Recent advances in the field of MRI have enabled tissue function to be probed noninvasively, and increasingly MRI is being used to assess cellular and molecular processes. For example, dynamic contrast-enhanced MRI has been used to assess tissue vascularity, diffusion-weighted imaging can quantify molecular movements of water in tissue compartments and MR spectroscopy provides a quantitative assessment of metabolite levels. A number of targeted contrast agents have been developed that bind specifically to receptors on the vascular endothelium or cell surface and there are several MR methods for labelling cells and tracking cellular movements. Hyperpolarization techniques have the capability of massively increasing the sensitivity of MRI and these have been used to image tissue pH, successful response to drug treatment as well as imaging the microstructure of the lungs. Although there are many challenges to be overcome before these techniques can be translated into routine paediatric imaging, they could potentially be used to aid diagnosis, predict disease outcome, target biopsies and determine treatment response noninvasively. (orig.)

  12. The Center for Integrated Molecular Brain Imaging (Cimbi) database

    DEFF Research Database (Denmark)

    Knudsen, Gitte M.; Jensen, Peter S.; Erritzoe, David

    2016-01-01

    We here describe a multimodality neuroimaging containing data from healthy volunteers and patients, acquired within the Lundbeck Foundation Center for Integrated Molecular Brain Imaging (Cimbi) in Copenhagen, Denmark. The data is of particular relevance for neurobiological research questions rela...... currently contains blood and in some instances saliva samples from about 500 healthy volunteers and 300 patients with e.g., major depression, dementia, substance abuse, obesity, and impulsive aggression. Data continue to be added to the Cimbi database and biobank....

  13. Molecular imaging of retinal endothelial injury in diabetic animals

    Directory of Open Access Journals (Sweden)

    Sonja Frimmel

    2017-01-01

    Conclusion: Results indicate that molecular imaging can be used to detect subtle changes in the diabetic retina prior to the occurrence of irreversible pathology. Thus, ICAM-1 could serve as a diagnostic target in patients with diabetes. This study provides a proof of principle for non-invasive subclinical diagnosis in experimental diabetic retinopathy. Further development of this technology could improve management of diabetic complications.

  14. Image Alignment for Multiple Camera High Dynamic Range Microscopy.

    Science.gov (United States)

    Eastwood, Brian S; Childs, Elisabeth C

    2012-01-09

    This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.

  15. Intelligent Design of Nano-Scale Molecular Imaging Agents

    Directory of Open Access Journals (Sweden)

    Takeaki Ozawa

    2012-12-01

    Full Text Available Visual representation and quantification of biological processes at the cellular and subcellular levels within living subjects are gaining great interest in life science to address frontier issues in pathology and physiology. As intact living subjects do not emit any optical signature, visual representation usually exploits nano-scale imaging agents as the source of image contrast. Many imaging agents have been developed for this purpose, some of which exert nonspecific, passive, and physical interaction with a target. Current research interest in molecular imaging has mainly shifted to fabrication of smartly integrated, specific, and versatile agents that emit fluorescence or luminescence as an optical readout. These agents include luminescent quantum dots (QDs, biofunctional antibodies, and multifunctional nanoparticles. Furthermore, genetically encoded nano-imaging agents embedding fluorescent proteins or luciferases are now gaining popularity. These agents are generated by integrative design of the components, such as luciferase, flexible linker, and receptor to exert a specific on–off switching in the complex context of living subjects. In the present review, we provide an overview of the basic concepts, smart design, and practical contribution of recent nano-scale imaging agents, especially with respect to genetically encoded imaging agents.

  16. Bioresponsive probes for molecular imaging:Concepts and in vivo applications

    OpenAIRE

    Duijnhoven, van, SMJ Sander; Robillard, MS Marc; Langereis, S Sander; Grüll, H Holger

    2015-01-01

    Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of molecular imaging probes, known as bioresponsive molecular probes, has been developed. These probes generally benefit from signal enhancement at the site of interaction with its target. There are mainly ...

  17. Featured Image: A Molecular Cloud Outside Our Galaxy

    Science.gov (United States)

    Kohler, Susanna

    2018-06-01

    What do molecular clouds look like outside of our own galaxy? See for yourself in the images above and below of N55, a molecular cloud located in the Large Magellanic Cloud (LMC). In a recent study led by Naslim Neelamkodan (Academia Sinica Institute of Astronomy and Astrophysics, Taiwan), a team of scientists explore N55 to determine how its cloud properties differ from clouds within the Milky Way. The image above reveals the distribution of infrared-emitting gas and dust observed in three bands by the Spitzer Space Telescope. Overplotted in cyan are observations from the Atacama Submillimeter Telescope Experiment tracing the clumpy, warm molecular gas. Below, new observations from the Atacama Large Millimeter/submillimeter Array (ALMA) reveal the sub-parsec-scale molecular clumps in greater detail, showing the correlation of massive clumps with Spitzer-identified young stellar objects (crosses). The study presented here indicates that this cloud in the LMC is the site of massive star formation, with properties similar to equivalent clouds in the Milky Way. To learn more about the authors findings, check out the article linked below.CitationNaslim N. et al 2018 ApJ 853 175. doi:10.3847/1538-4357/aaa5b0

  18. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

    Science.gov (United States)

    Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

    2017-03-01

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

  19. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    International Nuclear Information System (INIS)

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  20. A framework of region-based dynamic image fusion

    Institute of Scientific and Technical Information of China (English)

    WANG Zhong-hua; QIN Zheng; LIU Yu

    2007-01-01

    A new framework of region-based dynamic image fusion is proposed. First, the technique of target detection is applied to dynamic images (image sequences) to segment images into different targets and background regions. Then different fusion rules are employed in different regions so that the target information is preserved as much as possible. In addition, steerable non-separable wavelet frame transform is used in the process of multi-resolution analysis, so the system achieves favorable characters of orientation and invariant shift. Compared with other image fusion methods, experimental results showed that the proposed method has better capabilities of target recognition and preserves clear background information.