Molecular dynamics electric field crystallization simulations of paracetamol produce a new polymorph

C Parks, A Koswara, HH Tung, N Nere… - Crystal Growth & …, 2017 - ACS Publications
Using molecular dynamics simulations, we demonstrate the ability of high intensity, 1.5
V/nm, static electric fields to induce the formation of a new polymorph of paracetamol, one of …

Structure‐based analysis of thermodynamic and mechanical properties of cavity‐containing proteins–case study of plant pathogenesis‐related proteins of class 10

M Chwastyk, M Jaskolski, M Cieplak - The FEBS Journal, 2014 - Wiley Online Library
We provide theoretical comparisons of the physical properties of eighteen proteins with the
pathogenesis‐related proteins of class 10 (PR‐10) fold, which is characterized by a large …

Proteins at air–water interfaces: a coarse-grained model

M Cieplak, DB Allan, RL Leheny, DH Reich - Langmuir, 2014 - ACS Publications
We present a coarse-grained model to describe the adsorption and deformation of proteins
at an air–water interface. The interface is introduced empirically in the form of a localized …

Large conformational fluctuations of the multi-domain xylanase Z of Clostridium thermocellum

B Różycki, M Cieplak, M Czjzek - Journal of structural biology, 2015 - Elsevier
The cellulosome is a multi-enzyme machinery which efficiently degrades plant cell-wall
polysaccharides. The multiple domains of the cellulosome complexes are often tethered to …

Formation mechanism of metal–molecule–metal junctions: molecule-assisted migration on metal defects

D Thompson, J Liao, M Nolan, AJ Quinn… - The Journal of …, 2015 - ACS Publications
Activation energies, E a, measured from molecular exchange experiments are combined
with atomic-scale calculations to describe the migration of bare Au atoms and Au …

Peptide recognition capabilities of cellulose in molecular dynamics simulations

G Nawrocki, PA Cazade, D Thompson… - The Journal of …, 2015 - ACS Publications
Knowing the amino acid discriminating capacity of the surface of cellulose can be valuable
information toward the rational design and re-engineering of the cellulosome in order to …

An exploration of the universe of polyglutamine structures

À Gómez-Sicilia, M Sikora, M Cieplak… - PLoS computational …, 2015 - journals.plos.org
Deposits of misfolded proteins in the human brain are associated with the development of
many neurodegenerative diseases. Recent studies show that these proteins have common …

Denaturation of proteins near polar surfaces

A Starzyk, M Cieplak - The Journal of chemical physics, 2011 - pubs.aip.org
All-atom molecular dynamics simulations for proteins placed near a model mica surface
indicate existence of two types of evolution. One type leads to the surface-induced unfolding …

Proteins in the Electric Field near the Surface of Mica

A Starzyk, M Cieplak - The Journal of Chemical Physics, 2013 - pubs.aip.org
We elucidate the nature of the electric field produced by a model mica surface and show that
above some 0.4 nm it is nearly uniform and of order 12 V/nm. The presence of ions in the …

Self-assembly of gold nanocrystals into discrete coupled plasmonic structures

C Schopf, E Noonan, AJ Quinn, D Iacopino - Crystals, 2016 - mdpi.com
Development of methodologies for the controlled chemical assembly of nanoparticles into
plasmonic molecules of predictable spatial geometry is vital in order to harness novel …