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https://www.readbyqxmd.com/read/28640619/optimization-and-automation-of-the-construction-of-smooth-free-energy-profiles
#1
Jeremy Schofield
An adaptive procedure is introduced to construct smooth analytical profiles of the free energy along a reaction coordinate using sampled data from multiple biased simulations. The procedure is based upon identifying problematic regions encountered in maximum likelihood estimators of the profile where there are statistically relevant discrepancies between the empirical and parameterized cumulative distribution functions and preferentially improving the construction of the parametric profile in these regions...
June 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636916/structural-behavior-of-the-peptaibol-harzianin-hk-vi-in-a-dmpc-bilayer-insights-from-md-simulations
#2
Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S Ulrich, Tomáš Kubař
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636909/electric-field-induced-protein-translocation-via-a-conformational-transition-in-secdf-an-md-study
#3
Emel Ficici, Daun Jeong, Ioan Andricioaei
SecDF is an important component of the Sec protein translocation machinery embedded in the bacterial membrane, which is associated with many functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. Related studies suggest that SecDF undergoes functionally important conformational changes that involve mainly its P1-head domain and that these changes are coupled with the proton motive force (Δp)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636824/bicanonical-ab-initio-molecular-dynamics-for-open-systems
#4
Johannes Frenzel, Bernd Meyer, Dominik Marx
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both, nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636483/lumping-kinetics-of-abe-fermentation-wastewater-treatment-by-oleaginous-yeast-trichosporon-cutaneum
#5
Can Wang, Chao Huang, Xue-Fang Chen, Hai-Rong Zhang, Lian Xiong, Xiao-Mei Li, Hai-Jun Guo, Gao-Xiang Qi, Xiao-Qing Lin, Xin-De Chen
Lumping kinetics models were built for the biological treatment of ABE (acetone-butanol-ethanol) fermentation wastewater by oleaginous yeast Trichosporon cutaneum with different fermentation temperatures. Compared with high temperature (33°C, 306 K) and low temperature (23°C, 296 K), medium temperature (28°C, 301 K) was beneficial for the cell growth and COD degradation during the early stage of fermentation but the final yeast biomass and COD removal were influenced little. By lumping method, the materials in the bioconversion network were divided into five lumps (COD, lipid, polysaccharide, other intracellular products, other extracellular products), and the nine rate constants (k1-k9) for the models can well explain the bioconversion laws...
June 21, 2017: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/28636317/downsizing-proto-oncogene-cfos-to-short-helix-constrained-peptides-that-bind-jun
#6
Daniel Baxter, Samuel R Perry, Timothy A Hill, W Mei Kok, Nathan R Zaccai, R Leo Brady, David P Fairlie, Jody M Mason
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components...
June 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28636012/does-h4so5-exist
#7
Fernando Murillo, Alba Vargas-Caamal, Sudip Pan, José Luis Cabellos, Miguel J Mora-Fonz, Alvaro Muñoz-Castro, Albeiro Restrepo, Gabriel Merino
The possible existence of H4SO5 in aqueous sulfuric acid is analyzed in detail. For bare H4SO5, the computed free energy barrier for the exergonic transformation of H4SO5 into the H2SO4H2O complex is only 3.8 kcal mol(-1). The presence of water or sulfuric acid catalyzes the dehydration to such an extent that it becomes almost a barrierless process. In the gas phase, dehydration of H4SO5 is an autocatalytic reaction as the water molecule produced by the decomposition of one H4SO5 molecule induces further dissociation...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28635295/coarse-grained-models-of-aqueous-and-pure-liquid-alkanes
#8
Gaurav Gyawali, Samuel Sternfield, Revati Kumar, Steven W Rick
A model for linear alkanes is presented in which interaction sites are only on the carbon atoms and the range of the potential is reduced using the Stillinger-Weber potential. The model is optimized for aqueous and liquid alkane properties and can match thermodynamic and structural properties, including solvation free energies, liquid densities, and liquid/vapor and liquid/water surface tensions for alkanes over a range of lengths.The results for long alkanes indicates that such models can be useful as accurate, yet efficient, coarse-grained potentials for macromolecules in water and other environments...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28635289/exploring-the-drug-resistance-of-hcv-protease
#9
Garima Jindal, Dibyendu Mondal, Arieh Warshel
Hepatitis C virus (HCV) currently affects several million people across the globe. One of the major classes of drugs inhibits the NS3/4A protease of the polyprotein chain. Efficacy of these drugs is severely limited due to the high mutation rate that results in several genetically related quasispecies. The molecular mechanism of drug resistance is generally based on structural studies and binding free energies. However, prediction of new mutations requires a quantity that can define both binding free energy of the drug as well as the parameters (kcat and KM) for the natural substrate...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28634293/intrinsic-map-dynamics-exploration-for-uncharted-effective-free-energy-landscapes
#10
Eliodoro Chiavazzo, Roberto Covino, Ronald R Coifman, C William Gear, Anastasia S Georgiou, Gerhard Hummer, Ioannis G Kevrekidis
We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#11
Milosz Wieczór, Jacek Czub
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28632421/novel-urushiol-derivatives-as-hdac8-inhibitors-rational-design-virtual-screening-molecular-docking-and-molecular-dynamics-studies
#12
Hao Zhou, Chengzhang Wang, Tao Deng, Ran Tao, Wenjun Li
Three series of novel urushiol derivatives were designed by introducing a hydroxamic acid moiety into the tail of an alkyl side chain and substituents with differing electronic properties or steric bulk onto the benzene ring and alkyl side chain. The compounds' binding affinity towards HDAC8 was screened by Glide docking. The highest-scoring compounds were processed further with molecular docking, MD simulations and binding free energy studies to analyze the binding modes and mechanisms. Ten compounds had Glide scores of -8...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28631928/free-energy-of-nanoparticle-binding-to-multivalent-polymeric-substrates
#13
Chad Gu, Rob D Coalson, David Jasnow, Anton Zilman
Characterization of the interactions between nanosize ligands and polymeric substrates is important for predictive design of nanomaterials and in biophysical applications. The multivalent nature of the polymer-nanoparticle interaction and the dynamics of multiple internal conformations of the polymer chains makes it difficult to infer microscopic interactions from macroscopic binding assays. Using coarse-grained simulations, we estimate the free energy of binding between a nanoparticle and a surface-grafted polymeric substrate as a function of pertinent parameters such as polymer chain length, nanoparticle size, and microscopic polymer-nanoparticle attraction...
June 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28631801/morphology-of-elastic-nematic-liquid-crystal-membranes
#14
Pardis Rofouie, Damiano Pasini, Alejandro D Rey
Liquid crystalline phases found in many biological materials, such as actin, DNA, cellulose, and collagen can be responsible for the deformation of cell membranes. In this paper, cell membrane deformation is investigated through the coupling between liquid crystal anisotropy and membrane bending elasticity. The generalized shape equation for anisotropic interfaces, which resort to the Cahn-Hoffman capillarity vector, the Rapini-Papoular anchoring energy, and the Helfrich elastic energy, is applied to gain insight into the deformation of closed liquid crystal membranes...
June 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28631724/microscopic-origins-of-the-large-piezoelectricity-of-leadfree-ba-ca-zr-ti-o3
#15
Yousra Nahas, Alireza Akbarzadeh, Sergei Prokhorenko, Sergey Prosandeev, Raymond Walter, Igor Kornev, Jorge Íñiguez, L Bellaiche
In light of directives around the world to eliminate toxic materials in various technologies, finding lead-free materials with high piezoelectric responses constitutes an important current scientific goal. As such, the recent discovery of a large electromechanical conversion near room temperature in (1-x)Ba(Zr0.2Ti0.8)O3-x(Ba0.7Ca0.3)TiO3 compounds has directed attention to understanding its origin. Here, we report the development of a large-scale atomistic scheme providing a microscopic insight into this technologically promising material...
June 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28631123/modeling-solubility-of-co2-hydrocarbon-gas-in-ionic-liquid-emim-fap-using-aspen-plus-simulations
#16
Bishwadeep Bagchi, Sushmita Sati, Vidyasagar Shilapuram
The Peng-Robinson equation of state with quadratic van der Waals (vdW) mixing rule model was chosen to perform the thermodynamic calculations in Flash3 column of Aspen Plus to predict the solubility of CO2 or any one of the hydrocarbons (HCs) among methane, ethane, propane, and butane in an ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([emim][FAP]). Bubble point pressure, solubility, bubble point temperature, fugacity, and partial molar volume at infinite dilution were obtained from the simulations, and enthalpy of absorption, Gibbs free energy of solvation, and entropy change of absorption were estimated by thermodynamic relations...
June 19, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28630669/straight-round-the-twist-frustration-and-chirality-in-smectics-a
#17
Elisabetta A Matsumoto, Randall D Kamien, Gareth P Alexander
Frustration is a powerful mechanism in condensed matter systems, driving both order and complexity. In smectics, the frustration between macroscopic chirality and equally spaced layers generates textures characterized by a proliferation of defects. In this article, we study several different ground states of the chiral Landau-de Gennes free energy for a smectic liquid crystal. The standard theory finds the twist grain boundary (TGB) phase to be the ground state for chiral type II smectics. However, for very highly chiral systems, the hierarchical helical nanofilament phase can form and is stable over the TGB...
August 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28630476/first-principles-theory-of-the-hcp-fcc-phase-transition-in-cobalt
#18
Raquel Lizárraga, Fan Pan, Lars Bergqvist, Erik Holmström, Zsolt Gercsi, Levente Vitos
Identifying the forces that drive a phase transition is always challenging. The hcp-fcc phase transition that occurs in cobalt at ~700 K has not yet been fully understood, although early theoretical studies have suggested that magnetism plays a main role in the stabilization of the fcc phase at high temperatures. Here, we perform a first principles study of the free energies of these two phases, which we break into contributions arising from the vibration of the lattice, electronic and magnetic systems and volume expansion...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629618/conditioning-and-robustness-of-rna-boltzmann-sampling-under-thermodynamic-parameter-perturbations
#19
Emily Rogers, David Murrugarra, Christine Heitsch
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28628859/structural-and-functional-effects-of-nucleotide-variation-on-the-human-tb-drug-metabolizing-enzyme-arylamine-n-acetyltransferase-1
#20
Ruben Cloete, Wisdom A Akurugu, Cedric J Werely, Paul D van Helden, Alan Christoffels
The human arylamine N-acetyltransferase 1 (NAT1) enzyme plays a vital role in determining the duration of action of amine-containing drugs such as para-aminobenzoic acid (PABA) by influencing the balance between detoxification and metabolic activation of these drugs. Recently, four novel single nucleotide polymorphisms (SNPs) were identified within a South African mixed ancestry population. Modeling the effects of these SNPs within the structural protein was done to assess possible structure and function changes in the enzyme...
June 10, 2017: Journal of Molecular Graphics & Modelling
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