Related papers: Electrostatic Binding and Hydrophobic Collapse of …
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
Chemical functionalization of nanocarbons is an important strategy to produce electrochemical systems with higher energy/power density by generating surface functional groups with additional faradaic contribution, by increasing their…
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 study a single statistical amphiphilic copolymer chain AB in a selective solvent (e.g.water). Two situations are considered. In the annealed case, hydrophilic (A) and hydrophobic (B) monomers are at local chemical equilibrium and both…
Understanding strongly correlated systems is essential for advancing quantum chemistry and materials science, yet conventional methods like Density Functional Theory (DFT) often fail to capture their complex electronic behavior. To address…
Chemical crosslinking of collagen is a general strategy to reproduce macroscale tissue properties in physiological environment. However, simultaneous control of protein conformation, material properties and biofunctionality is highly…
We investigate the collapse kinetics of charged polymers (polyelectrolytes) induced by counterion condensation using coarse-grained molecular dynamics simulations. Under good solvent conditions, polyelectrolytes above the critical charge…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We investigate the dependency of electrostatic interaction forces on applied potentials in Electrostatic Force Microscopy (EFM) as well as in related local potentiometry techniques like Kelvin Probe Microscopy (KPM). The approximated…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
Unravelling the origins of single-atom catalyst reactivity is a central challenge in heterogeneous catalysis research. A key question is whether the activity arises solely from atomic isolation or from distinct structural and electronic…
The solvation of charged, nanometer-sized spherical solutes in water, and the effective, solvent-induced force between two such solutes are investigated by constant temperature and pressure Molecular Dynamics simulations of model solutes…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…
This paper compares simulation results and experimental published data concerning the interaction between $\alpha_2\beta_1$ integrin and collagen.This phenomenon is characterized by a competition among steric, reciprocal orientation…
Fundamental mechanisms of energy storage, corrosion, sensing, and multiple biological functionalities are directly coupled to electrical processes and ionic dynamics at solid-liquid interfaces. In many cases, these processes are spatially…
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles…
The ever-growing intersection of quantum electrodynamics (QED) and molecular processes has shown remarkable and unanticipated advancements in altering molecular properties and reactivity by exploiting light-matter couplings. In recent…