Related papers: Diffusion-limited unbinding of small peptides from…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
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…
Consistently atomistic understanding of the mechanism behind the intriguing behavior of low-dimensional systems including monatomic chains, hollow tubes, surface skins, nanocavities, nanowires, and nanograins has long been a high challenge.…
A cell dynamics method for domain separation of diblock copolymers (DBCPs) interacting with nanoparticles (NPs) whose diffusion coefficients depend on chain configuration is proposed for self-assembly of DBCP/NP composites. Increasing NP…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex ($P_1$$P_2$). The joint distribution $P(\tau_1,\tau_2)$ of unbinding lifetimes $\tau_1$ and $\tau_2$ measurable in…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
Exact and approximate expressions for thermodynamic characteristics of heated matter, which consists of particles with finite mass-widths, are constructed. They are expressed in terms of Fermi/Bose distributions and spectral functions,…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…