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Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations

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Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

John Maddocks, Rahul Sharma, Alessandro Samuele Patelli

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

2023

Molecular simulations allow to investigate the behaviour of materials at the atomistic level, shedding light on phenomena that cannot be directly observed in experiments. Accurate results can be obtained with ab initio methods, while simulations of large-s ...

EPFL2021

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water. The method consists of two additive contributions: (i) ...

ROYAL SOC CHEMISTRY2020

The free energy plays a fundamental role in theories of phase transformations and microstructure evolution. It encodes the thermodynamic coupling between different fields, such as mechanics and chemistry, within continuum descriptions of non-equilibrium ma ...

Elsevier2020

Vase-Kite Equilibrium of Resorcin[4]arene Cavitands Investigated Using Molecular Dynamics Simulations with Ball-and-Stick Local Elevation Umbrella Sampling

Jovana Milic

A key feature of resorcin[4]arene cavitands is their ability to switch between a closed/contracted (Vase) and an open/expanded (Kite) conformation. The mechanism and dynamics of this interconversion remains, however, elusive. In the present study, the Vase ...

2019

Assessment of Approximate Methods for Anharmonic Free Energies

Michele Ceriotti, Venkat Kapil, Edgar Albert Engel, Mariana Rossi Carvalho

Quantitative evaluation of the thermodynamic properties of materials—most notably their stability, as measured by the free energy—must take into account the role of thermal and zero-point energy fluctuations. While these effects can easily be estimated wit ...

2019

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

John Maddocks, Daiva Petkeviciute, Marco Pasi

We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structura ...

Oxford University Press (OUP)2019

Ab Initio Flexible Force Field for Metal-Organic Frameworks Using Dummy Model Coordination Bonds

Berend Smit, Seyedmohamad Moosavi, Matthew David Witman, Sudabeh Jawahery, Nakul Rampal

We present force fields developed from periodic density functional theory (DFT) calculations that can be used in classical molecular simulations to model M MOF-74 (M = Co, Fe, Mg, Mn, Ni, Zn) and its extended linker analogs. Our force fields are based on c ...

2019