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Journal of Physical Chemistry B, ISSN 1520-6106, 01/2019, Volume 123, Issue 2, pp. 468 - 479
Molecular dynamics simulations were employed to study the properties of G-quadruplex and i-motif secondary DNA structures formed within the canonical telomere... 
CHEMISTRY, PHYSICAL | FORCE-FIELD | SEQUENCE
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2013, Volume 9, Issue 9, pp. 3878 - 3888
We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled... 
UBIQUITIN | RESOLUTION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | FORCE-FIELD | ALGORITHMS | PHYSICS | EFFICIENT | GRAPHICS PROCESSING UNITS
Journal Article
CHEMICAL COMMUNICATIONS, ISSN 1359-7345, 2013, Volume 49, Issue 10, pp. 981 - 983
A novel approach in molecular docking was successfully used to reproduce protein-ligand experimental geometries. When dealing with halogenated compounds the... 
FORCE-FIELD | ATOMS | HALOGEN | CHEMISTRY, MULTIDISCIPLINARY
Journal Article
JOURNAL OF APPLIED PHYSICS, ISSN 0021-8979, 03/2015, Volume 117, Issue 12
We present X-ray diffraction and Raman spectroscopy investigations of a (100)-oriented (AlxGa1-x)(2)O-3 thin film on MgO (100) and bulk-like ceramics in... 
SYSTEM | PHYSICS, APPLIED | OXIDE | FORCE-FIELD
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 01/2008, Volume 4, Issue 1, pp. 116 - 122
By removing the fastest degrees of freedom, constraints allow for an increase of the time step in molecular simulations. In the last decade parallel... 
DYNAMICS SIMULATIONS | RATTLE | SHAKE | ALGORITHM | EQUATIONS | VERSION | FORCE-FIELD | SYSTEMS | CHEMISTRY, MULTIDISCIPLINARY | ALKANES
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 12/2009, Volume 131, Issue 51, pp. 18198 - 18199
A diverse collection of 14 metal-organic frameworks (MOFs) was screened for CO2 capture from flue gas using a combined experimental and modeling approach.... 
STORAGE | REMOVAL | CO2 | FORCE-FIELD | SIMULATIONS | ADSORPTION | CHEMISTRY, MULTIDISCIPLINARY | Chemical properties | Adsorption | Structure | Analysis | Carbon dioxide | Organometallic compounds
Journal Article
Nature Communications, ISSN 2041-1723, 09/2015, Volume 6, Issue 1, pp. 8335 - 8335
The intrinsic defects in reduced graphene oxide (rGO) formed during reduction processes can act as nanopores, making rGO a promising ultrathin-film membrane... 
FORCE-FIELD | CARBON-DIOXIDE | WATER DESALINATION | MULTIDISCIPLINARY SCIENCES | NATURAL-GAS | PERMEATION
Journal Article
NATURE, ISSN 0028-0836, 08/2015, Volume 524, Issue 7565, pp. 315 - 315
Activation of the mu-opioid receptor (mu OR) is responsible for the efficacy of the most effective analgesics. To shed light on the structural basis for mu OR... 
CRYSTALLIZING MEMBRANE-PROTEINS | COMPLEX | LIPIDIC MESOPHASES | PROTEIN-COUPLED RECEPTOR | MULTIDISCIPLINARY SCIENCES | FORCE-FIELD | ADRENERGIC-RECEPTOR | MOLECULAR-DYNAMICS SIMULATIONS | CHARMM | MICE LACKING | MUSCARINIC ACETYLCHOLINE-RECEPTOR
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 01/2016, Volume 37, Issue 3, pp. 354 - 365
This article describes a revised version 56A6 CARBO_R of the GROMOS 56A6 CARBO force field for hexopyranose‐based carbohydrates. The simulated properties of... 
hexopyranose | GROMOS force field | molecular dynamics | ring conformers | carbohydrate | Methylation
Journal Article
Physical Review B - Condensed Matter and Materials Physics, ISSN 1098-0121, 05/2011, Volume 83, Issue 19
Using molecular dynamics simulations and model graphene layers in an organic matrix we demonstrate that interfacial thermal resistance determined via thermal... 
PHYSICS, CONDENSED MATTER | FORCE-FIELD | VIBRATIONAL-RELAXATION | HEAT-FLOW
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 07/2008, Volume 130, Issue 26, pp. 8359 - 8365
The pi-stacked interactions in some explosive crystal packing are discussed. Taking a typical. pi-stacked explosive 2,4,6-trinitrobenzene-1,3,5-triamine (TATB)... 
FORCE-FIELD | HMX | 1,3,5-TRIAMINO-2,4,6-TRINITROBENZENE | TATB | CHEMISTRY, MULTIDISCIPLINARY | AB-INITIO
Journal Article
Carbon, ISSN 0008-6223, 12/2019, Volume 154, pp. 192 - 202
The diffusion of point defects after irradiation events in graphite is considered using high temperature molecular dynamics and adaptive kinetic Monte Carlo.... 
Long-time scale dynamics | Reactive force field | Graphite | Defects
Journal Article
Nature Communications, ISSN 2041-1723, 01/2014, Volume 5, Issue 1, pp. 3186 - 3186
It is important from a fundamental standpoint and for practical applications to understand how the mechanical properties of graphene are influenced by defects.... 
SOLAR-CELLS | ELASTIC PROPERTIES | MULTIDISCIPLINARY SCIENCES | RAMAN-SPECTROSCOPY | REACTIVE FORCE-FIELD | ELECTRODES | GRAPHITE OXIDE | MECHANICAL-PROPERTIES | TRANSPARENT | SHEETS | CARBON NANOTUBES
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 05/2018, Volume 122, Issue 21, pp. 5291 - 5299
We recently showed that the time-structure-based independent component analysis method from Markov state model literature provided a set of variationally... 
CHEMISTRY, PHYSICAL | METADYNAMICS | FORCE-FIELD | MOLECULAR-DYNAMICS SIMULATION | KINETICS | PERMEATION
Journal Article
Fuel, ISSN 0016-2361, 11/2019, Volume 256, p. 115884
Compared with the isothermal pyrolysis, non-isothermal pyrolysis is more accurate and efficient, and closer to the actual reaction process. To better... 
Lignite | Heating rate | Reactive force field | Pyrolysis mechanism
Journal Article
Biophysical Journal, ISSN 0006-3495, 01/2012, Volume 102, Issue 3, pp. 736a - 736a
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 04/2019, Volume 123, Issue 15, pp. 3199 - 3209
By applying an electric field to an insulating membrane, movement of charged particles through a nanopore can be induced. The measured ionic current reports on... 
TRANSLOCATION | MOLECULAR-DYNAMICS | SPECTROSCOPY | KINETICS | EQUILIBRIUM | CHEMISTRY, PHYSICAL | FORCE-FIELD
Journal Article
JOURNAL OF MEDICINAL CHEMISTRY, ISSN 0022-2623, 02/2019, Volume 62, Issue 4, pp. 1999 - 2007
Assaying lipolytic enzymes is extremely challenging because they act on water-insoluble lipid substrates, which are normally components of micelles, vesicles,... 
MOLECULAR-DYNAMICS | POTENT | CHEMISTRY, MEDICINAL | ENZYMES | FORCE-FIELD | LIPIDS
Journal Article
ACS Macro Letters, ISSN 2161-1653, 02/2019, Volume 8, Issue 2, pp. 123 - 127
We utilize atomistic molecular dynamics (MD) simulations to study local structural changes inside a polyelectrolyte complex consisting of... 
FORCE-FIELD | POLYMER SCIENCE | EFFICIENT | SCATTERING
Journal Article
Journal of Physical Chemistry A, ISSN 1089-5639, 02/2019, Volume 123, Issue 6, pp. 1131 - 1139
We present a method based on kinetic molecular theory that identifies reactions of various molecularities in molecular dynamics (MD) simulations of bulk gases.... 
REACTIVE FORCE-FIELD | CHEMISTRY, PHYSICAL | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
Journal Article
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