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Poly(N-isopropylacrylamide) (PNIPAM) is a temperature-responsive polymer that undergoes large volumetric deformations through a transition from a swollen to a collapsed state at the volume phase transition temperature (VPTT). Locally, these…
Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
Electrostatic interactions in polymeric systems are responsible for a wide range of liquid-liquid phase transitions that are of importance for biology and materials science. Such transitions are referred to as complex coacervation, and…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
We investigate the structural and topological properties of hydrophobic homopolymer chains in aqueous solutions using molecular dynamics simulations and circuit topology (CT) analysis. By combining geometric observables, such as radius of…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
We study the bending rigidity of highly charged stiff polyelectrolytes, for both a single chain and many chains forming a bundle. A theory is developed to account for the interplay between competitive binding of counterions and charge…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Thermo-responsive hydrogels are a promising material for creating controllable actuators for use in micro-scale devices, since they expand and contract significantly (absorbing or expelling fluid) in response to relatively small temperature…
We present a simple yet generic model for the behavior of a system of many surface-attached flexible polymers with rigid side chains. Beyond its potential application in describing the dynamics of the extracellular matrix of mammalian…
Persistent homology (PH) was applied to probe the structural changes of glasses under shear. PH associates each local atomistic structure in an atomistic configuration to a geometric object, namely, a hole, and evaluates the robustness of…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
Partial pair-correlation functions of colloidal suspensions with continuous polydispersity can be challenging to characterize from optical microscopy or computer simulation data due to inadequate sampling. As a result, it is common to adopt…