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We investigate the crystallization of crosslinked and entangled polymers under external deformation using a coarse-grained poly(vinyl alcohol) (CG-PVA) model and molecular dynamics simulations. Following uniaxial deformation, the systems…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
In this work, we present a generalization of extended persistent homology to filtrations of graded sub-groups by defining relative homology in this setting. Our work provides a more comprehensive and flexible approach to get an algebraic…
The effects of thermal coupling between two thin liquid layers, separated by a gas layer, are discussed. The liquid layers undergo long-wavelength instabilities driven by gravitational and thermocapillary stresses. To study the dynamics,…
Motion of protein drops on crystallization media during routine handling is a major factor affecting the reproducibility of crystallization conditions. Drop stability can be enhanced by chemical patterning to more effectively pin the drop's…
We study the combined influence of amino acid composition and chain length on the thermal stability of protein structures. A new parameterization of the internal free energy is considered, as the sum of hydrophobic effect, hydrogen-bond and…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
We study the dynamical regimes of a density-stratified fluid confined between isothermal no-slip top and bottom boundaries (at temperatures $T_t$ and $T_b$) via direct numerical simulation. The thermal expansion coefficient of the fluid is…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
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…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
We review briefly several approaches used to investigate the stability of stripe phases in high temperature superconductors, where charge inhomogeneities arise from competing kinetic and magnetic energies. The mechanism of stripe formation,…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
The stabilization of liquid biological products is a complex task that depends on the chemical composition of both the active ingredient and any excipients in solution. Frequently, a large number of unique excipients are required to…
The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
Jamming is a phenomenon shared by a wide variety of systems, such as granular materials, foams, and glasses in their high density regime. This has motivated the development of a theoretical framework capable of explaining many of their…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…