scholarly journals CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins

Symmetry ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2401
Author(s):  
Alistair Turcan ◽  
Anna Zivkovic ◽  
Dylan Thompson ◽  
Lorraine Wong ◽  
Lauren Johnson ◽  
...  
Keyword(s):  
Drug Development ◽  
Data Visualization ◽  
Conformational Changes ◽  
Web Server ◽  
Coarse Grained ◽  
Analysis Techniques ◽  
Fine Grained ◽  
Protein Conformational Changes ◽  
Rigidity Analysis ◽  
Rigid Cluster

Elucidating protein rigidity offers insights about protein conformational changes. An understanding of protein motion can help speed drug development, and provide general insights into the dynamic behaviors of biomolecules. Existing rigidity analysis techniques employ fine-grained, all-atom modeling, which has a costly run-time, particularly for proteins made up of more than 500 residues. In this work, we introduce coarse-grained rigidity analysis, and showcase that it provides flexibility information about a protein that is similar in accuracy to an all-atom modeling approach. We assess the accuracy of the coarse-grained method relative to an all-atom approach via a comparison metric that reasons about the largest rigid clusters of the two methods. The apparent symmetry between the all-atom and coarse-grained methods yields very similar results, but the coarse-grained method routinely exhibits 40% reduced run-times. The CGRAP web server outputs rigid cluster information, and provides data visualization capabilities, including a interactive protein visualizer.

Coarse-Grained Molecular Dynamics Simulations of Sugar Transport Across Lactose Permease

2015 ◽  
Author(s):  
Yead Jewel ◽  
Prashanta Dutta ◽  
Jin Liu
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Active Transport ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Sugar Transport ◽  
Potential Of Mean Force ◽  
Coarse Grained ◽  
Lactose Permease ◽  
Protein Conformational Changes

Sugar (one of the critical nutrition elements for all life forms) transport across the cell membranes play essential roles in a wide range of living organism. One of the most important active transport (against the sugar concentration) mechanisms is facilitated by the transmembrane transporter proteins, such as the Escherichia coli lactose permease (LacY) proteins. Active transport of sugar molecules with LacY proteins requires a proton gradient and a sequence of complicated protein conformational changes. However, the exact molecular mechanisms and the protein structural information involved in the transport process are largely unknown. All atom atomistic simulations are able to provide full details but are limited to relative small length and time scales due to the computational cost. The protein conformational changes during sugar transport across LacY are large scale structural reorganization and inaccessible to all atom simulations. In this work, we investigate the molecular mechanisms and conformational changes during sugar transport using coarse-grained molecular dynamics (CGMD) simulations. In our coarse-grained force field, we follow the procedures developed by Han et al. [1, 2], in which the protein model is united-atom based and each heavy atom together with the attached hydrogen atoms is represented by one site, then the protein force filed is coupled with the MARTINI [3] water and lipid force fields. This hybrid force field takes the advantage of the efficiency of MARTINI force field for the environment (water and lipid), while retaining the detailed conformational information for the proteins. Specifically, we develop the new force fields for interactions between sugar molecules and protein by matching the potential of mean force between all-atom and coarse-grained models. Then we validate our force field by comparing the potential of mean force for a glucose interaction with a carbohydrate binding protein from our new force field, with the results from all atom simulations. After validation, we implement the force field for sugar transport across LacY proteins. Through our simulations we are able to capture the formation/breakage of the important hydrogen bonds and salt bridges, which are crucial to the overall conformational changes of LacY.

Correlation between dislocation, grain boundary and interface of duplex SS in stress corrosion cracking(SCC)

1990 ◽  
Vol 48 (4) ◽  
pp. 928-929
Author(s):  
Wang Zheng-fang ◽  
Z.F. Wang
Keyword(s):  
Stainless Steel ◽  
Thermal Cycle ◽  
Secondary Phase ◽  
Corrosion Cracking ◽  
Coarse Grained ◽  
Test Environment ◽  
Fine Grained ◽  
Evaluation Test ◽  
Welding Thermal Cycle ◽  
Micro Analysis

The main purpose of this study highlights on the evaluation of chloride SCC resistance of the material,duplex stainless steel,OOCr18Ni5Mo3Si2 (18-5Mo) and its welded coarse grained zone(CGZ).18-5Mo is a dual phases (A+F) stainless steel with yield strength:512N/mm2 .The proportion of secondary Phase(A phase) accounts for 30-35% of the total with fine grained and homogeneously distributed A and F phases(Fig.1).After being welded by a specific welding thermal cycle to the material,i.e. Tmax=1350°C and t8/5=20s,microstructure may change from fine grained morphology to coarse grained morphology and from homogeneously distributed of A phase to a concentration of A phase(Fig.2).Meanwhile,the proportion of A phase reduced from 35% to 5-10°o.For this reason it is known as welded coarse grained zone(CGZ).In association with difference of microstructure between base metal and welded CGZ,so chloride SCC resistance also differ from each other.Test procedures:Constant load tensile test(CLTT) were performed for recording Esce-t curve by which corrosion cracking growth can be described, tf,fractured time,can also be recorded by the test which is taken as a electrochemical behavior and mechanical property for SCC resistance evaluation. Test environment:143°C boiling 42%MgCl2 solution is used.Besides, micro analysis were conducted with light microscopy(LM),SEM,TEM,and Auger energy spectrum(AES) so as to reveal the correlation between the data generated by the CLTT results and micro analysis.

scholarly journals Protein conformational changes and myelin solubilization by anion-detergent solutions

FEBS Letters ◽  
1992 ◽  
Vol 309 (3) ◽  
pp. 376-380 ◽  
Author(s):  
Jaime Monreal ◽  
Pedro Carmona ◽  
Pilar Regueiro ◽  
Ricardo S. Diaz
Keyword(s):  
Conformational Changes ◽  
Protein Conformational Changes ◽  
Detergent Solutions

scholarly journals Balanced Sparsity for Efficient DNN Inference on GPU

2019 ◽  
Vol 33 ◽  
pp. 5676-5683 ◽  
Author(s):  
Zhuliang Yao ◽  
Shijie Cao ◽  
Wencong Xiao ◽  
Chen Zhang ◽  
Lanshun Nie
Keyword(s):  
Deep Neural Networks ◽  
General Purpose ◽  
Coarse Grained ◽  
Efficient Computation ◽  
Model Accuracy ◽  
Sparse Model ◽  
Model Inference ◽  
Fine Grained ◽  
Practical Inference ◽  
Speed Up

In trained deep neural networks, unstructured pruning can reduce redundant weights to lower storage cost. However, it requires the customization of hardwares to speed up practical inference. Another trend accelerates sparse model inference on general-purpose hardwares by adopting coarse-grained sparsity to prune or regularize consecutive weights for efficient computation. But this method often sacrifices model accuracy. In this paper, we propose a novel fine-grained sparsity approach, Balanced Sparsity, to achieve high model accuracy with commercial hardwares efficiently. Our approach adapts to high parallelism property of GPU, showing incredible potential for sparsity in the widely deployment of deep learning services. Experiment results show that Balanced Sparsity achieves up to 3.1x practical speedup for model inference on GPU, while retains the same high model accuracy as finegrained sparsity.

scholarly journals Submarine lava deltas of the 2018 eruption of Kīlauea volcano

2021 ◽  
Vol 83 (4) ◽  
Author(s):  
S. Adam Soule ◽  
Michael Zoeller ◽  
Carolyn Parcheta
Keyword(s):  
Grain Size ◽  
Pore Pressure ◽  
Mechanistic Model ◽  
Large Fraction ◽  
Volcanic Hazards ◽  
Lava Flows ◽  
Coarse Grained ◽  
Fine Grained ◽  
Fine Grain ◽  
Delta Formation

AbstractHawaiian and other ocean island lava flows that reach the coastline can deposit significant volumes of lava in submarine deltas. The catastrophic collapse of these deltas represents one of the most significant, but least predictable, volcanic hazards at ocean islands. The volume of lava deposited below sea level in delta-forming eruptions and the mechanisms of delta construction and destruction are rarely documented. Here, we report on bathymetric surveys and ROV observations following the Kīlauea 2018 eruption that, along with a comparison to the deltas formed at Pu‘u ‘Ō‘ō over the past decade, provide new insight into delta formation. Bathymetric differencing reveals that the 2018 deltas contain more than half of the total volume of lava erupted. In addition, we find that the 2018 deltas are comprised largely of coarse-grained volcanic breccias and intact lava flows, which contrast with those at Pu‘u ‘Ō‘ō that contain a large fraction of fine-grained hyaloclastite. We attribute this difference to less efficient fragmentation of the 2018 ‘a‘ā flows leading to fragmentation by collapse rather than hydrovolcanic explosion. We suggest a mechanistic model where the characteristic grain size influences the form and stability of the delta with fine grain size deltas (Pu‘u ‘Ō‘ō) experiencing larger landslides with greater run-out supported by increased pore pressure and with coarse grain size deltas (Kīlauea 2018) experiencing smaller landslides that quickly stop as the pore pressure rapidly dissipates. This difference, if validated for other lava deltas, would provide a means to assess potential delta stability in future eruptions.

scholarly journals A cooperative DDoS attack detection scheme based on entropy and ensemble learning in SDN

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Shanshan Yu ◽  
Jicheng Zhang ◽  
Ju Liu ◽  
Xiaoqing Zhang ◽  
Yafeng Li ◽  
...  
Keyword(s):  
Ensemble Learning ◽  
Denial Of Service ◽  
Attack Detection ◽  
Coarse Grained ◽  
Communication Overhead ◽  
Detection Scheme ◽  
Fine Grained ◽  
Ddos Attack ◽  
Network Status ◽  
Ddos Attack Detection

AbstractIn order to solve the problem of distributed denial of service (DDoS) attack detection in software-defined network, we proposed a cooperative DDoS attack detection scheme based on entropy and ensemble learning. This method sets up a coarse-grained preliminary detection module based on entropy in the edge switch to monitor the network status in real time and report to the controller if any abnormality is found. Simultaneously, a fine-grained precise attack detection module is designed in the controller, and a ensemble learning-based algorithm is utilized to further identify abnormal traffic accurately. In this framework, the idle computing capability of edge switches is fully utilized with the design idea of edge computing to offload part of the detection task from the control plane to the data plane innovatively. Simulation results of two common DDoS attack methods, ICMP and SYN, show that the system can effectively detect DDoS attacks and greatly reduce the southbound communication overhead and the burden of the controller as well as the detection delay of the attacks.

Rheology of hydrocarbon gels

1950 ◽  
Vol 200 (1061) ◽  
pp. 183-188 ◽  
Keyword(s):  
Mechanical Properties ◽  
Experimental Measurement ◽  
Theoretical Basis ◽  
Continuous Media ◽  
Point Of View ◽  
Coarse Grained ◽  
Testing Instrument ◽  
Fine Grained ◽  
Mineral Oils ◽  
Space And Time

Hydrocarbon gels contain a number of materials, such as rubber, greases, saponified mineral oils, etc., of great interest for various engineering purposes. Specific requirements in mechanical properties have been met by producing gels in appropriately chosen patterns of constituent components of visible, colloidal, molecular and atomic sizes, ranging from coarse-grained aggregates, represented by sponges, foams, emulsions, etc.; to fine-grained and apparently homogeneous ones, represented by optically clear compounds. The engineer who has to deal with the whole range of such materials will adopt a macroscopic point of view, based on an apparent continuity of all the material structures and of the distributions in space and time of the displacements and forces occurring under mechanical actions. It has been possible to determine these distributions in the framework of a comprehensive scheme in which the fundamental principles of the mechanics of continuous media provide the theoretical basis, and a testing instrument of new design, termed Rheogoniometer, the means of experimental measurement (Weissenberg 1931, 1934, 1946, 1947, 1948).

Sign in / Sign up

Export Citation Format

Share Document