Results 1 to 10 of about 154,477 (340)

Intramolecular Force Mapping at Room Temperature. [PDF]

ACS Nano, 2023
Acquisition of dense, three-dimensional, force fields with intramolecular resolution via noncontact atomic force microscopy (NC-AFM) has yielded enormous progress in our ability to characterize molecular and two-dimensional materials at the atomic scale. To date, intramolecular force mapping has been performed exclusively at cryogenic temperatures, due
Brown T, Blowey PJ, Henry J, Sweetman A.
europepmc   +5 more sources

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching. [PDF]

J Chem Theory Comput, 2018
The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles generated at one level of theory (e.g., "low") not being good approximations of ensembles at the other (e.g., "high"). Numerous strategies have been devised to mitigate this issue.
Hudson PS, Boresch S, Rogers DM, Woodcock HL.   +3 more
europepmc   +7 more sources

Theory of mechanical unfolding of homopolymer globule: all-or-none transition in force-clamp mode vs phase coexistence in position-clamp mode [PDF]

Macromolecules 44 (20), 8270 (2011), 2012
Equilibrium mechanical unfolding of a globule formed by long flexible homopolymer chain collapsed in a poor solvent and subjected to an extensional force f (force-clamp mode) or extensional deformation D (position-clamp mode) is studied theoretically. Our analysis, like all previous analysis of this problem, shows that the globule behaves essentially ...
Alexey A. Polotsky, Balescu R., Borgia A., Cooke R., Craig A., Elizaveta E. Smolyakova, Forman J. R., Grosberg A. Y., Halperin A., Halperin A., Landau L. D., Lifshitz I. M., Meglio A., Moffitt J. R., Neumann R. M., Oberhauser A. F., Polotsky A. A., Polotsky A. A., Polotsky A. A., Puchner E. M., Rayleigh L., Samori B., Schlierf M., Schrödinger E., Sinha S., Skvortsov A. M., Süzen M., Tatiana M. Birshtein, Williams M. C., Winkler R. G.   +29 more
arxiv   +3 more sources

Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function [PDF]

eLife, 2015
Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance.
Jason C Bell, Bian Liu, Stephen C Kowalczykowski   +2 more
doaj   +4 more sources

Cooperative Dynamics in Unentangled Polymer Fluids [PDF]

, 2001
We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE, are in quantitative agreement with computer simulation data.
A. Kolinski, F. J. Vesely, J. P. Hansen, K. Kremer, K. S. Schweizer, K. S. Schweizer, M. Bixon, M. Doi, M. Guenza, M. Guenza, P. J. Flory, P.-G. de Gennes   +11 more
arxiv   +3 more sources

On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase [PDF]

J. Chem. Phys., 126 (2007) 204307, 2007
Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas phase simulations.
Hansmann, U. H. E., Nadler, W., Wei, Y.
arxiv   +3 more sources

Tetrahedrality, hydrogen bonding and the density anomaly of the central force water model. A Monte Carlo study [PDF]

Condensed Matter Physics, 2021
Monte Carlo computer simulations in the canonical and grand canonical statistical ensemble were used to explore the properties of the central force (CF1) water model.
V. Ravnik, B. Hribar-Lee, O. Pizio, M. Lukšič   +3 more
doaj   +2 more sources

Nonlinear Elasticity of Single Collapsed Polyelectrolytes [PDF]

, 2004
Nonlinear elastic responses of short and stiff polyelectrolytes are investigated by dynamic simulations on a single molecule level. When a polyelectrolyte condensate undergoes a mechanical unfolding, two types of force-extension curves, i.e., a force plateau and a stick-release pattern, are observed depending on the strength of the electrostatic ...
C. G. Baumann, G. E. Plum, G. S. Manning, Hirofumi Wada, J. Israelachvili, M. Doi, Masaki Sano, P. G. de Gennes, R. R. Netz, W. M. Gelbart, Yoshihiro Murayama   +10 more
arxiv   +3 more sources

Pauli's Principle in Probe Microscopy [PDF]

arXiv, 2014
Exceptionally clear images of intramolecular structure can be attained in dynamic force microscopy through the combination of a passivated tip apex and operation in what has become known as the "Pauli exclusion regime" of the tip-sample interaction. We discuss, from an experimentalist's perspective, a number of aspects of the exclusion principle which ...
A Riss, A Sweetman, AJ Weymouth, C Weiss, C Weiss, CW Wilson, CW Wilson, CW Wilson, D Dieks, D Dieks, DG Oteyza de, E Fermi, EH Lieb, EH Lieb, EH Lieb, EJ Baerends, F Mohn, F Wilczek, FJ Giessibl, G Beylkin, G Kichin, J Welker, J Zhang, JC Slater, JC Slater, JE Sader, JE Sader, JW Rohlf, L Gross, L Gross, L Kantorovich, M Fleischhauer, M Massimi, MAM Versteegh, MV Berry, N Moll, N Pavlicek, NS Ginsberg, PAM Dirac, R Pawlak, R Temirov, RP Feynman, W Pauli, W Pauli, WJ Mullin, WM De Muynck, Y Omar, Z Sun   +47 more
arxiv   +5 more sources

Molecular Dynamics Study of the Green Solvent Polyethylene Glycol with Water Impurities [PDF]

Molecules
Polyethylene glycol (PEG) is one of the environmentally benign solvent options for green chemistry. It readily absorbs water when exposed to the atmosphere.
Markus M. Hoffmann, Matthew D. Too, Nathaniel A. Paddock, Robin Horstmann, Sebastian Kloth, Michael Vogel, Gerd Buntkowsky   +6 more
doaj   +2 more sources