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Journal of Physics Condensed Matter, ISSN 0953-8984, 01/2018, Volume 30, Issue 4, pp. 043002 - 043002
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 06/2019, Volume 150, Issue 21, p. 214114
The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables... 
Alanine | System dynamics | Simulation | Approximants | Machine learning | Molecular dynamics | Eigenvectors | Orthogonality | Sampling | Regularization | Complex systems
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 08/2019, Volume 151, Issue 6
Time-lagged autoencoders (TAEs) have been proposed as a deep learning regression-based approach to the discovery of slow modes in dynamical systems. However, a... 
Alanine | Neural networks | Machine learning | Nonlinear analysis | Markov processes | Regression analysis | Dynamical systems
Journal Article
Soft Matter, ISSN 1744-683X, 2016, Volume 12, Issue 34, pp. 7119 - 7135
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 11/2018, Volume 122, Issue 44, pp. 10219 - 10236
Self-assembling peptides containing aromatic groups are an attractive target for bioelectronic materials design because of their ease of manufacture,... 
INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Journal Article
Soft Matter, ISSN 1744-683X, 2015, Volume 11, Issue 41, pp. 8141 - 8153
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 02/2017, Volume 121, Issue 7, pp. 1684 - 1706
Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of... 
DYNAMICS SIMULATIONS | POLYMERS | MODELS | KINETICS | MINERALIZATION | CHEMISTRY, PHYSICAL | FORCE-FIELD | NANOSTRUCTURES | PROTEINS | EFFICIENT | EQUATION | Molecular simulation | Usage | Peptides | Optical properties | Analysis | Chemical bonds | Chemical properties | Electric properties | Self assembly | Optoelectronics | Computer simulation | Aggregates | Dynamics | Mathematical models | Assembly
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 12/2018, Volume 122, Issue 50, pp. 11931 - 11952
The stability and folding of proteins is governed by the underlying single-molecule free energy surface (smFES) mapping the free energy of the molecule as a... 
ATTRACTORS | DESIGN | VARIATIONAL APPROACH | FREE-ENERGY LANDSCAPES | NONLINEAR DIMENSIONALITY REDUCTION | DYNAMICS | CHEMISTRY, PHYSICAL | TRP-CAGE | DIFFUSION MAPS | SIMULATIONS | FORCED SYSTEMS
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 05/2009, Volume 113, Issue 18, pp. 6405 - 6414
We employ molecular dynamics simulations to study the solubility and molecular conformations of n-alkane chains in water. We find nearly exponential decrease... 
DYNAMICS SIMULATIONS | BETA-HAIRPIN | MUTUAL SOLUBILITIES | HYDROCARBONS | CHEMISTRY, PHYSICAL | HYDROPHOBIC COLLAPSE | SYSTEMS | PHASE-EQUILIBRIA | MONTE-CARLO-SIMULATION | EWALD SUMMATION | AQUEOUS-SOLUTION | Molecular dynamics | Alkanes | Usage | Research | Properties | Solubility
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 06/2018, Volume 122, Issue 25, pp. 6627 - 6647
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 06/2019, Volume 141, Issue 24, pp. 9693 - 9700
Journal Article
Molecular Simulation, ISSN 0892-7022, 07/2018, Volume 44, Issue 11, p. 930
Self-assembling oligopeptides present a means to fabricate biocompatible supramolecular aggregates with engineered electronic and optical functionality. We... 
supramolecular peptides | self-assembly | molecular dynamics simulation | quantitative structure-property relationships | conjugated oligopeptides
Journal Article
Current Opinion in Colloid & Interface Science, ISSN 1359-0294, 11/2018, Volume 38, pp. 204 - 213
Antimicrobial peptides (AMPs) collectively constitute a key component of the host innate immune system. They span a diverse space of sequences and can be... 
Toll-like receptors | Innate immunity | Membrane curvature | Antimicrobial peptides | Machine learning | DOUBLE-STRANDED-RNA | PARAMYXOVIRUS PIV5 | CHEMISTRY, PHYSICAL | ALPHA-DEFENSINS | INNATE LYMPHOID-CELLS | MITOCHONDRIAL FISSION | HOST-DEFENSE PEPTIDES | INFLUENZA-A VIRUS | STRUCTURAL BASIS | DYNAMIN-RELATED GTPASE | Peptides
Journal Article
Molecular Simulation, ISSN 0892-7022, 07/2018, Volume 44, Issue 11, pp. 930 - 945
Self-assembling oligopeptides present a means to fabricate biocompatible supramolecular aggregates with engineered electronic and optical functionality. We... 
supramolecular peptides | self-assembly | quantitative structure-property relationships | conjugated oligopeptides | molecular dynamics simulation | Self assembly | Aggregates | Computer simulation | Stacking | Nondestructive testing | Machine learning | Assembling | Inspection | Molecular dynamics | Biocompatibility | Mathematical models | Molecular chains
Journal Article
ORGANIC & BIOMOLECULAR CHEMISTRY, ISSN 1477-0520, 07/2017, Volume 15, Issue 26, pp. 5484 - 5502
Self-assembled nanoaggregates of pi-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups... 
BIOMOLECULAR SIMULATIONS | POLYMERS | MOLECULAR-DYNAMICS | OLIGOPEPTIDES | CHEMISTRY, ORGANIC | CONSTANT-PH | FORCE-FIELD | COAGULATION | NANOSTRUCTURES | MODEL | AGGREGATION
Journal Article
Applied and Computational Harmonic Analysis, ISSN 1063-5203, 07/2019, Volume 47, Issue 1, pp. 190 - 211
Diffusion maps are a nonlinear manifold learning technique based on harmonic analysis of a diffusion process over the data. Out-of-sample extensions with... 
Molecular simulation | Harmonic analysis | Diffusion maps | Spectral graph theory | Nonlinear dimensionality reduction | MATHEMATICS, APPLIED | MOLECULAR-DYNAMICS | POTENTIAL FUNCTIONS | ALGORITHMS | EIGENMAPS | SPACE | FREE-ENERGY LANDSCAPES | EXPLORATION | PROTEINS
Journal Article