36 research outputs found
Thermal Behavior Of Dielectric Materials During Rapid Heating
No full textThe objective of this research is to understand the temperature variation in dielectric materials of different geometry. The work is divided into three major segments. The Thermal Wave model has been taken into consideration as the classical Fourier law of heat conduction breaks down when a dielectric material of sub-micron geometry is heated rapidly. The first partof the work discusses primarily about the temperature distribution in a semi-infinite dielectric material, followed by the temperature profile in a finite body (plate) and finally mathematical formulation is presented for a two-layered body. The thermal wave equation is used because in dielectric materials the lag time due to temperature ( ) is much less than the lag time due to heat flux ( ), and hence all the terms describing the effects of in the governing equation used for expressing the phenomena of Hyperbolic Heat Conduction in a material can be neglected. Boundary conditions of first and second kind are applied to the thermal wave equation for all three cases that are discussed later in the study. The classical Laplace Transform method has been used as a tool to analyze the mathematical models for all the illustrations presented in the study. Analytical solutions are obtained for semi-infinite and finite bodies for different boundary conditions and a mathematical formulation has been presented to calculate the heat flux at the interface for a two-layered dielectric body. Due to large complexity of the problem and intense use of algebra several Mathematica subroutines are developed to compute and examine the thermal behavior of dielectric materials during rapid heating
Simulation Data for Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination
No full text<p>This is supporting information for an upcoming research manuscript. The uploaded tarball contains the directory structure needed to reproduce the simulations conducted to support the forthcoming article. The directory structure has three primary subdirectories, Alphafold which contains the initial structure predictions, Build, which has the Tcl scripts in VMD to assemble the system, and Simulation, which has the simulations themselves and the analysis. Since there is a limit to the file sizes that can be stored on Zenodo, we exclude many files to fit under the limit. The command to create the tarball was: <code>tar --exclude=LukeSim --exclude="*trr" --exclude="*dcd" --exclude="*GO*" --exclude="*HPR*" --exclude="*PGP*" --exclude="*GAT*" --exclude="*#" --exclude="*ppm" --exclude="*BAK" --exclude="*oldpgp*" -zcvf glykthermostable.tar.gz Thermostability/</code></p>
<p>While the full trajectories are too large to be provided, reduced trajectories of only the protein component can be found in the <code>Thermostability/Simulation/Analysis/prottrajs</code> path. Files with the <code>.js</code> extension can be read via VMD.</p>
Analytical Temperature Distribution in a Multi-Layer Tissue Structure in the Presence of a Tumor
No full textLongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems
No full textWe develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations
Atomistic Origins of Biomass Recalcitrance in Organosolv Pretreatment
No full textSecondary plant cell walls are made from three common biopolymers, cellulose, lignin, and hemicellulose, representing a critical feedstock for sustainable biomaterial production. Separating lignocellulosic biomass components for use in tailored sustainable energy and materials applications is challenging, as the biopolymers are in close proximity within the plant secondary cell wall. Organic solvents are used to pretreat recalcitrant biomass and separate the interacting polymers, solubilizing the lignin fraction for lignin-first valorization approaches. However, no single organosolv pretreatment approach has proven superior for heterogeneous biomass samples. Simulation offers a complementary atomic view into interactions between biomass components, resolving mechanistic hypotheses for how biomass composition influences separations processes. Using molecular dynamics simulations, we quantify lignin-cellulose interactions through binding free energies determined from 300 lignin polymer models in nine solvent environments, across four crystalline cellulose faces, with an aggregate simulation time of nearly 154 microseconds. The binding free energy determined from simulation categorizes the solvents. For poor lignin solvents, all lignin polymers bind strongly to cellulose. By contrast, polar protic solvents such as methanol and ethanol favor the unbinding between lignin and cellulose in all conditions, regardless of charge for the lignin monomer tested. Aprotic organic solvents separate lignin from cellulose only for uncharged lignin monomers, with charged lignin monomers associating to cellulose. While polar protic solvents are most effective at breaking apart lignin-cellulose interactions for charged lignin species, solvent dynamics highlight that there is no single optimal solvent to facilitate lignin-cellulose separation, particularly as some solvents demonstrate greater effectiveness for skewed S:G ratios. Instead, the optimal solvent for a given lignin sample will depend on the lignin compound and the net charge for the lignin polymers
Thermal Modeling of Memory Access Operations in Microprocessors
No full textA large fraction of energy consumed in modern microelectronic devices and systems is taken up by memory access operations, which is expected to cause significant temperature rise. Since memory access operations are very short in duration, this is expected to inherently be a transient thermal phenomenon. Despite the critical importance of thermal management in microelectronics, not much work exists on understanding the nature of thermal transport during memory access operations. In this work, a mathematical model to predict the transient temperature rise within a 3D memory chip is presented. Most heat-generating memory access processes occur over a short timescale for which the thermal penetration depth is shorter than the die thickness. This enables the modeling of such processes independent of the nature of chip cooling by treating the chip as a semi-infinite medium. A semi-infinite Green’s function model is developed for one bank of memory on a single layer of a block of the memory chip. This model is validated against finite element simulation results. Validation is also carried out by comparison of the model against the analytical solution for a limiting case. The analytical model is used to analyze transient thermal effects of various memory access processes for multiple banks. These results will help develop an understanding of optimal layouts and processes for 3D memory chips, eventually leading to co-design tools that simultaneously improve thermal and electrical performance of 3D memory chips.</jats:p
Simulation Input Data for "Atomic Origins of Biomass Recalcitrance in Organic Solvents"
No full textThis is the reduced data behind an upcoming manuscript investigating lignocellulosic interactions in plant secondary wall, when exposed to different organic solvent pretreatment. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:
tar -zcvf lignincelluloseindustrialsolvent.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*log" --exclude="*[0-9].out" --exclude="*npz" --exclude="*pkl" --exclude="*npy" --exclude="*png" --exclude="*bmim*" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*txt" --exclude="*state_prev.cpt" --exclude="*ppm" --exclude="Simulations" FaceDifferences
Within the FaceDifferences directory, there are 2 primary subdirectories:
Build contains the scripts and files to build the individual lignin cellulose in organic solvent molecular systems.
NewSolventSimulations contains the all-atom MD simulation inputs and the analysis scripts (subdirectory Analysis
Non-Arrhenius Reaction-Diffusion Kinetics for Protein Inactivation over a Large Temperature Range
No full textUnderstanding
protein folding and unfolding has been a long-standing
fundamental question and has important applications in manipulating
protein activity in biological systems. Experimental investigations
of protein unfolding have been predominately conducted by small temperature
perturbations (e.g., temperature jump), while molecular simulations
are limited to small time scales (microseconds) and high temperatures
to observe unfolding. Thus, it remains unclear how fast a protein
unfolds irreversibly and loses function (i.e., inactivation) across
a large temperature range. In this work, using nanosecond pulsed heating
of individual plasmonic nanoparticles to create precise localized
heating, we examine the protein inactivation kinetics at extremely
high temperatures. Connecting this with protein inactivation measurements
at low temperatures, we observe that the kinetics of protein unfolding
is less sensitive to temperature change at the higher temperatures,
which significantly departs from the Arrhenius behavior extrapolated
from low temperatures. To account for this effect, we propose a reaction-diffusion
model that modifies the temperature-dependence of protein inactivation
by introducing a diffusion limit. Analysis of the reaction-diffusion
model provides general guidelines in the behavior of protein inactivation
(reaction-limited, transition, diffusion-limited) across a large temperature
range from physiological temperature to extremely high temperatures.
We further demonstrate that the reaction-diffusion model is particularly
useful for designing optimal operating conditions for protein photoinactivation.
The experimentally validated reaction-diffusion kinetics of protein
unfolding is an important step toward understanding protein-inactivation
kinetics over a large temperature range. It has important applications
including molecular hyperthermia and calls for future studies to examine
this model for other protein molecules
Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"
No full textThe tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.
All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.
The source code is publicly available on GitHub: https://github.com/radical-collaboration/MDFF-EnTK
The preprint of this research is submitted on bioRxiv, doi: https://doi.org/10.1101/2021.12.07.471672
To obtain maximum compression of the data, the tar command used to generate this tarball was:
GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo
