301 citations · 2.5k across the 73 of their papers we have counts for
8 papers · 1 filter
Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles
Łukasz Mioduszewski, Jakub Bednarz, Mateusz Chwastyk +1
We present a coarse-grained C-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential…
First-principles design of nanomachines
Jayanth R. Banavar, Marek Cieplak, Trinh Xuan Hoang +1
Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nano-machines. We show that the crucial ingredients for a…
Nanoscale fluid flows in the vicinity of patterned surfaces
Marek Cieplak, Joel Koplik, Jayanth R. Banavar
Molecular dynamics simulations of dense and rarefied fluids comprising small chain molecules in chemically patterned nano-channels predict a novel switching from Poiseuille to plug…
Thermal Folding and Mechanical Unfolding Pathways of Protein Secondary Structures
Marek Cieplak, Trinh Xuan Hoang, Mark O. Robbins
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the s…
Protein threading by learning
Iksoo Chang, Marek Cieplak, Ruxandra I. Dima +2
Using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complet…
Delineation of the Native Basin in Continuum Models of Proteins
Mai Suan Li, Marek Cieplak
We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories em…
Folding in two-dimenensional off-lattice models of proteins
Mai Suan Li, Marek Cieplak
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic…
Simple models of proteins with repulsive non-native contacts
Mai Suan Li, Marek Cieplak
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non…