301 citations · 2.5k across the 73 of their papers we have counts for
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Folding of Proteins in Go Models with Angular Interactions
Marek Cieplak, Trinh Xuan Hoang
Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g…
Effects of Pore Walls and Randomness on Phase Transitions in Porous Media
Marek Cieplak, Amos Maritan, Michael R. Swift +2
We study spin models within the mean field approximation to elucidate the topology of the phase diagrams of systems modeling the liquid-vapor transition and the separation of He$^3…
Universality classes in folding times of proteins
Marek Cieplak, Trinh Xuan Hoang
Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider th…
Prediction of Protein Secondary Structures From Conformational Biases
Trinh Xuan Hoang, Marek Cieplak, Jayanth R. Banavar +1
We use LINUS, a procedure developed by Srinivasan and Rose, to provide a physical interpretation of and to predict the secondary structures of proteins. The secondary structure typ…
Folding and Stretching in a Go-like Model of Titin
Marek Cieplak, Trinh Xuan Hoang, Mark O. Robbins
Mechanical stretching of the I27 domain of titin and of its double and triple repeats are studied through molecular dynamics simulations of a Go-like model with Lennard-Jones conta…
Motion of grains, droplets, and bubbles in fluid-filled nano-pores
Nazar Sushko, Marek Cieplak
Molecular dynamics studies of nono-sized rigid grains, droplets and bubbles in nano-sized pores indicate that the drag force may have a hydrodynamic form if the moving object is de…
Kinetic non-optimality and vibrational stability of proteins
Marek Cieplak, Trinh Xuan Hoang
Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied unde…
Dynamic modeling of gene expression data
Neal S. Holter, Amos Maritan, Marek Cieplak +2
We describe the time evolution of gene expression levels by using a time translational matrix to predict future expression levels of genes based on their expression levels at some…
Amino acid classes and the protein folding problem
Marek Cieplak, Neal S. Holter, Amos Maritan +1
We present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully…
Sequencing of folding events in Go-like proteins
Trinh Xuan Hoang, Marek Cieplak
We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a G…
Molecular dynamics of flows in the Knudsen regime
Marek Cieplak, Joel Koplik, Jayanth R. Banavar
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations…
Spin analogs of proteins: scaling of "folding" properties
Trinh Xuan Hoang, Nazar Sushko, Mai Suan Li +1
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determin…
Molecular dynamics of folding of secondary structures in Go-type models of proteins
Trinh Xuan Hoang, Marek Cieplak
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-amino…
Scaling of folding properties in simple models of proteins
Marek Cieplak, Trinh Xuan Hoang, Mai Suan Li
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native sta…
Energy landscapes, supergraphs, and "folding funnels" in spin systems
Piotr Garstecki, Trinh Xuan Hoang, Marek Cieplak
Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph…
Coarse grained description of the protein folding
Marek Cieplak, Trinh Xuan Hoang
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between…
Master equation approach to protein folding
Marek Cieplak, Malte Henkel, Jayanth R. Banavar
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state…
Protein folding and models of dynamics on the lattice
Trinh Xuan Hoang, Marek Cieplak
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinet…
Master equation approach to protein folding and kinetic traps
Marek Cieplak, Malte Henkel, Jan Karbowski +1
The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the…
Models of Fractal River Basins
Marek Cieplak, Achille Giacometti, Amos Maritan +3
Two distinct models for self-similar and self-affine river basins are numerically investigated. They yield fractal aggregation patterns following non-trivial power laws in experime…