Search results for "molecules"

Endothelial adhesion molecules in essential hypertension: response to arginine infusion

2001

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

2018

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both impli…

Equilibrium swelling properties of polyampholytic hydrogels

1996

The role of counter ions and ion dissociation in establishing the equilibrium swelling of balanced and unbalanced polyampholytic hydrogels has been investigated experimentally and theoretically. The swelling dependence on both the net charge offset and the external bath salt concentration has been examined using an acrylamide based polyampholytic hydrogels. By careful consideration of the swelling kinetics, we illustrate the effects of ion dissociation equilibria and counter ion shielding in polyampholytic hydrogels near their balance point where both polyelectrolyte and polyampholyte effects are present. The theory considers a Flory type swelling model where the Coulombic interactions betw…

Self-Assembly of Supramolecular Polymers of N-Centered Triarylamine Trisamides in the Light of Circular Dichroism: Reaching Consensus between Electro…

2020

The self-assembly of chiral supramolecular polymers is an intricate process that spans a wide range of length scales. Circular dichroism techniques are ideal to study this process as they provide information on the molecular scale but are at the same time also sensitive probes of the long-range interactions that control the growth and morphology of these polymers. As yet, Electronic Circular Dichroism that uses electronic transitions as a probe has by far been the method of choice while Vibrational Circular Dichroism, which uses vibrational transitions to probe structure, is much less employed. Here, we report experimental and theoretical studies of the self-assembly of helical supramolecul…

Inhibition of FTSJ1, a tryptophan tRNA-specific 2’-O-methyltransferase as possible mechanism to readthrough premature termination codons (UGAs) of th…

2022

Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10 % of the mutations affecting the CFTR gene are "stop" mutations, which generate a Premature Termination Codon (PTC), thus resulting in the synthesis of a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, that is the capacity of the ribosome to skip a PTC, thus generating a full-length protein. “TRIDs” are molecules exerting ribosome readthrough and for some of them the mechanism of action is still under debate. By in silico analysis as well as in vitro studies, we investigate a possible mechanism of action (MOA) by whic…

Effect of nanostructuration on the spin crossover transition in crystalline ultrathin films† †Electronic supplementary information (ESI) available: M…

2019

Film thickness and microstructure critically affect the spin crossover transition of a 2D coordination polymer.

Dynamical Stark Effect in the nu(2)/nu(4) Vibrational Polyad of SiH(4): Theory and Observation.

2000

We report a theoretical and experimental investigation of the dynamical Stark effect in a tetrahedral molecule, silane (SiH(4)). We use a tetrahedral formalism and Floquet theory to calculate the absorption spectra for the molecule dressed by an intense nonresonant pulsed laser. Experimentally, the dynamical Stark effect is observed for transitions of the nu(2)/nu(4) vibrational polyad of SiH(4) by means of nanosecond diode laser absorption spectroscopy and a Nd:YAG laser excitation. Copyright 2000 Academic Press.

Simulations and Experiments in Protein Folding

2014

The interplay between simulations and experiments of protein folding has largely contributed to the elucidation of many important aspects of the phenomenon. In this chapter, I briefly describe the experiments which provide information on the kinetics of the protein folding process, and help to characterize the folding transition state. Then, I show how to probe the kinetics of protein folding using molecular dynamics simulations, how to compare the simulations with the experiments and how to help and rationalize the latter, ultimately offering a molecular picture of the process. After the production of suitable molecular dynamics simulation data in the form of trajectories, the procedure in…

All-or-none proteinlike folding transition of a flexible homopolymer chain.

2009

Here we report a first-order all-or-none transition from an expanded coil to a compact crystallite for a flexible polymer chain. Wang-Landau sampling is used to construct the complete density of states for square-well chains up to length 256. Analysis within both the microcanonical and canonical ensembles shows a direct freezing transition for finite length chains with sufficiently short-range interactions. This type of transition is a distinctive feature of "one-step" protein folding and our findings demonstrate that a simple homopolymer model can exhibit protein-folding thermodynamics.

Estimation of formamide harmonic and anharmonic modes in the Kohn-Sham limit using the polarization consistent basis sets.

2010

Formamide harmonic and anharmonic frequencies of fundamental vibrations in the gas phase and in several solvents were successfully estimated in the B3LYP Kohn-Sham complete basis set limit (KS CBS). CBS results were obtained by extrapolating a power function (two-parameter formula) to the results calculated with polarization-consistent basis sets. Anharmonic corrections using the second order perturbation treatment (PT2) and hybrid B3LYP functional combined with polarization consistent pc-n (n = 0, 1, 2, 3, 4) and several Pople’s basis sets were analyzed for all fundamental formamide vibrational modes in the gas phase and solution. Solvent effects were modeled within a PCM method. The anhar…