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Journal of Applied Physics, ISSN 0021-8979, 07/2019, Volume 126, Issue 4, p. 45103
As a stacking form of ultrathin polymer films, multilayer nanostructures are of great interest in various applications. Coarse-grained molecular dynamics... 
PHYSICS, APPLIED | MODULUS | MECHANICAL-PROPERTIES | GROMACS | BLENDS | PREDICTION
Journal Article
RSC Advances, ISSN 2046-2069, 2019, Volume 9, Issue 9, pp. 5197 - 5205
Molecular dynamics simulations of neutral gold nanoparticles (AuNPs) interacting with dipalmitoylphosphatidylcholine (DPPC) and... 
SIZE | DYNAMICS | MEMBRANES | PENETRATION | GROMACS | CHEMISTRY, MULTIDISCIPLINARY | PERMEATION | INSIGHTS
Journal Article
CHEMISTRY OF MATERIALS, ISSN 0897-4756, 09/2019, Volume 31, Issue 17, pp. 6605 - 6614
We explore several potential dopant-free triphenylamine-based hole transport materials for perovskite solar cells by combining two design strategies: (1)... 
MOBILITY | MATERIALS SCIENCE, MULTIDISCIPLINARY | PEROVSKITE SOLAR-CELLS | LENGTH | CRYSTALS | CHEMISTRY, PHYSICAL | GENERAL FORCE-FIELD | GROMACS
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 07/2019, Volume 123, Issue 29, pp. 6314 - 6330
The uniform size and complex chemical topology of the pores formed by self-assembled amphiphilic molecules such as liquid crystals make them promising... 
1 NM PORES | MOLECULAR-DYNAMICS | RADIUS | MODELS | POLYMER MEMBRANES | CHEMISTRY, PHYSICAL | DIFFUSION | FABRICATION | SOLVATION | GROMACS | SOLVENT
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 06/2019, Volume 141, Issue 24, pp. 9655 - 9663
In this study, we investigated the molecular dynamics of polyrotaxane (PR), composed of alpha-cyclodextrins (CDs) and a poly(ethylene glycol) (PEG) axial... 
SELF-DIFFUSION | GELS | FORCE | MOBILITY | CYCLODEXTRIN | SPIN-ECHO | VISCOSITY | ROTAXANES | GROMACS | EFFICIENT | CHEMISTRY, MULTIDISCIPLINARY
Journal Article
Applied Physics Letters, ISSN 0003-6951, 02/2017, Volume 110, Issue 9, p. 92903
Despite its importance, carrier conduction in electrical insulators is poorly understood. This work presents a computational study of hole conduction in single... 
CHAIN | PHYSICS, APPLIED | ELECTRON-TRANSFER | OCTADECANE | CHARGE-TRANSPORT | SIMULATIONS | MODEL | GROMACS | POLYETHYLENE | N-C36H74
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 04/2019, Volume 123, Issue 14, pp. 3118 - 3123
An essential step of nanoliposome formation in an aqueous lipid solution is the transition from discoidal lipid aggregate (bicelle) to vesicle. We investigate... 
ULTRASOUND | SIZE | COARSE-GRAINED MODEL | CHEMISTRY, PHYSICAL | BILAYERS | LIPOSOMES | DOMAINS | GROMACS | WATER
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 08/2011, Volume 32, Issue 11, pp. 2359 - 2368
Journal Article
JOURNAL OF CHEMICAL INFORMATION AND MODELING, ISSN 1549-9596, 08/2019, Volume 59, Issue 8, pp. 3359 - 3364
The configuration of most current academic high-performance computing (HPC) resources tends to enforce ways of working with, and thinking about, molecular... 
COMPUTER SCIENCE, INFORMATION SYSTEMS | CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | GROMACS | CHEMISTRY, MULTIDISCIPLINARY
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 12/2018, Volume 122, Issue 49, pp. 11807 - 11816
We introduce the combinatorial averaged transient structure (CATS) clustering method as a means to cluster protein structure ensembles based on the... 
RECOGNITION | ALGORITHM | FUZZY | DYNAMICS | CHEMISTRY, PHYSICAL | NEURAL-NETWORK | TAU | SIMULATION | PROTEINS | GROMACS | AGGREGATION
Journal Article
Computer Physics Communications, ISSN 0010-4655, 02/2016, Volume 199, pp. 1 - 7
In molecular dynamics simulations, sufficient sampling is of key importance and a continuous challenge in the field. The coarse grain Martini force field has... 
Gromacs | Verlet neighbor search | Coarse-Grain | Lennard-Jones | MOLECULAR-DYNAMICS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | COARSE-GRAINED MODEL | SIMULATIONS | PHYSICS, MATHEMATICAL | Energy conservation | Liquids | Partitioning | Computer simulation | Molecular dynamics | Sampling | Lennard-Jones potential | Standards | Free energy
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 05/2018, Volume 122, Issue 21, pp. 5316 - 5326
Matrix metalloproteinase-1 (MMP-1) is a zinc-dependent protease that catalyzes hydrolysis of interstitial collagens. A previously reported X-ray... 
MOLECULAR-DYNAMICS | DOMAIN | COLLAGEN | MECHANISM | MMP-1 | HYDROLYSIS | CHEMISTRY, PHYSICAL | SIMULATION | GROMACS | REGION
Journal Article
Computer Physics Communications, ISSN 0010-4655, 07/2018, Volume 228, pp. 209 - 218
Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However,... 
LAMMPS | VASP | Molecular dynamics | Correlation function | Neutron scattering | GROMACS | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | PACKAGE | PHYSICS, MATHEMATICAL
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2018, Volume 14, Issue 4, pp. 2042 - 2051
Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, fast interconversion between a more stable... 
SUBSTITUENT | COMPLEX | STATES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | SIMULATIONS | DFTB3 | GROMACS | EFFICIENT | SOLVENT
Journal Article
BMC Research Notes, ISSN 1756-0500, 2012, Volume 5, Issue 1, pp. 367 - 367
Journal Article
BIOPHYSICAL JOURNAL, ISSN 0006-3495, 02/2017, Volume 112, Issue 3, pp. 450 - 459
The N-terminal tail of histone H4 is an indispensable mediator for inter-nucleosome interaction, which is required for chromatin fiber condensation. H4K16... 
CHROMATIN FIBER | INTERNUCLEOSOME INTERACTIONS | ANGSTROM RESOLUTION | H4 TAIL | MOLECULAR SIMULATION | BIOPHYSICS | H4-K16 ACETYLATION | GROMACS | CORE PARTICLE | HAMILTONIAN REPLICA EXCHANGE | NUCLEIC-ACIDS
Journal Article
The journal of physical chemistry. B, ISSN 1520-6106, 08/2019, Volume 123, Issue 37, pp. 7794 - 7800
Phosphorylation of glucose is the prime step in sugar metabolism and energy storage. Two key glucose phosphates are involved, that is, glucose 6-phosphate... 
MOLECULAR-DYNAMICS | ANOMERIC SPECIFICITY | ACID | SPECTROSCOPY | RECOGNITION | QUANTUM | CHEMISTRY, PHYSICAL | ACTIVITY SPECTRA | SIMULATION | GLUCOKINASE | GROMACS
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 06/2019, Volume 123, Issue 23, pp. 4833 - 4843
Multimodal chromatography uses small ligands with multiple modes of interaction, e.g., charged, hydrophobic or hydrogen bonding, to separate proteins from... 
TEMPERATURE | FIELD | MODE | CHEMISTRY, PHYSICAL | ADSORPTION | SELECTIVITY | GROMACS | ALANINE DIPEPTIDE | BINDING REGIONS | DEPENDENCE | INSIGHTS | BASIC BIOLOGICAL SCIENCES
Journal Article
RSC ADVANCES, ISSN 2046-2069, 2019, Volume 9, Issue 19, pp. 10914 - 10926
The poor burning resistance of cotton necessitates the control of its pyrolytic reactions, but many approaches have relied on the use of synthetically... 
FOURIER-TRANSFORM | RAMAN-SPECTROSCOPY | RESISTANCE | FABRICS | FLAME RETARDANTS | NONWOVENS | PYROLYSIS | GROMACS | CHEMISTRY, MULTIDISCIPLINARY | COTTON | EXPOSURE
Journal Article
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS, ISSN 0927-7757, 10/2019, Volume 578, p. 123635
Molecular dynamics (MD) simulations provide molecular level information about the interaction of organic molecules with the solid surfaces. There has been much... 
MONTE-CARLO | GLASS | Adsorption | Molecular dynamics | CHEMISTRY, PHYSICAL | POTENTIAL FUNCTIONS | FORCES | SIMULATIONS | Organic molecules | Silica | FREE-ENERGY | GROMACS
Journal Article
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