Uncovering One-Dimensional Reaction Coordinate that Underlies Structure-Function Relationship of Proteins

2022 ◽  
Author(s):  
Shanshan Wu ◽  
Huiyu Li ◽  
Ao Ma
Keyword(s):  
Protein Dynamics ◽  
Computational Cost ◽  
Reaction Coordinate ◽  
Functional Protein ◽  
Complex Molecules ◽  
One Dimensional ◽  
Protein Functions ◽  
Function Relationship ◽  
The One ◽  
Relationship Of

Understanding the mechanism of functional protein dynamics is critical to understanding protein functions. Reaction coordinates is a central topic in protein dynamics and the grail is to find the one-dimensional reaction coordinate that can fully determine the value of committor (i.e. the reaction probability in configuration space) for any protein configuration. We present a powerful new method that can, for the first time, identify the rigorous one-dimensional reaction coordinate in complex molecules. This one-dimensional reaction coordinate is determined by a fundamental mechanical operator--the generalized work functional. This method only requires modest computational cost and can be readily applied to large molecules. Most importantly, the generalized work functional is the physical origin of the collectivity in functional protein dynamics and provides a tentative roadmap that connects the structure of a protein to its function.

scholarly journals One-Dimensional Vacuum Steady Seepage Model of Unsaturated Soil and Finite Difference Solution

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Feng Huang ◽  
Jianguo Lyu ◽  
Guihe Wang ◽  
Hongyan Liu
Keyword(s):  
Finite Difference ◽  
Unsaturated Soil ◽  
Vacuum Pressure ◽  
Vacuum Field ◽  
One Dimensional ◽  
Steady Seepage ◽  
Basic Equations ◽  
The One ◽  
Seepage Law ◽  
Relationship Of

Vacuum tube dewatering method and light well point method have been widely used in engineering dewatering and foundation treatment. However, there is little research on the calculation method of unsaturated seepage under the effect of vacuum pressure which is generated by the vacuum well. In view of this, the one-dimensional (1D) steady seepage law of unsaturated soil in vacuum field has been analyzed based on Darcy’s law, basic equations, and finite difference method. First, the gravity drainage ability is analyzed. The analysis presents that much unsaturated water can not be drained off only by gravity effect because of surface tension. Second, the unsaturated vacuum seepage equations are built up in conditions of flux boundary and waterhead boundary. Finally, two examples are analyzed based on the relationship of matric suction and permeability coefficient after boundary conditions are determined. The results show that vacuum pressure will significantly enhance the drainage ability of unsaturated water by improving the hydraulic gradient of unsaturated water.

Verification of a Finite Element Method for Solving One-Dimensional Equations of Blood Flow Incorporating a Viscoelastic Wall Model

2009 ◽  
Author(s):  
Rashmi Raghu ◽  
Charles A. Taylor
Keyword(s):  
Blood Flow ◽  
Surgical Planning ◽  
Computational Cost ◽  
Three Dimensional ◽  
Momentum Equation ◽  
Cross Sectional ◽  
One Dimensional ◽  
The One ◽  
Modeling Flow ◽  
Three Dimensional Simulations

The one-dimensional (1-D) equations of blood flow consist of the conservation of mass equation, balance of momentum equation and a wall constitutive equation with arterial flow rate, cross-sectional area and pressure as the variables. 1-D models of blood flow enable the solution of large networks of blood vessels including wall deformability. Their level of detail is appropriate for applications such as modeling flow and pressure waves in surgical planning and their computational cost is low compared to three-dimensional simulations.

A Smart Actuator Design for Multiple Bio-Reagent Mixing in a High Pressure Optical Cell for Bio-Physical Research Applications

2008 ◽  
Author(s):  
Oliver Xie ◽  
Parkson Lee-Gau Chong ◽  
Jack Zhou
Keyword(s):  
High Pressure ◽  
Structure Function ◽  
Biological Molecules ◽  
Optical Cell ◽  
Helical Springs ◽  
Smart Actuator ◽  
Function Relationship ◽  
The One ◽  
Relationship Of ◽  
Actuator Design

During the past two decades, bio-physicists have had an increasing interest in finding out what happens when two bio-material solutions are mixed under high pressure. Compared to temperature, pressure makes more contributions to our fundamental understanding of the structure-function relationship of biological systems, because pressure produces only volume changes under isothermal conditions, and pressure results can then be interpreted in a more straightforward manner. Window-type High Pressure Optical Cell (HPOC) such as the one designed by Paladini and Weber have provided biophysicists with a powerful tool to understanding the structure-function relationships of biological molecules. However, the conventional HPOC is only good for single solution testing and does not allow for quick mixing and stirring of additional components while the specimen is under pressure. This research is to thoroughly study the feasibility of Shape Memory Alloy (SMA) as an actuator to perform mixing and agitation functions; and five types of SMA actuators were designed, simulated and tested for unplugging and mixing purposes. To conduct this research, SMA helical springs were fabricated in house according to the design requirements. With different combinations of SMA tensile springs, SMA compressive spring and biasing spring, significant ranges of vibration were developed. To further improving mixing process, a unique hybrid design of SMA as an actuator to unplug the stopper and micromotor as a stir device to agitate the solutions was developed. Rapid mixing of 95% of total solution in 10 seconds was achieved under 300 bars. A new HPOC was designed according to the new cuvette with its new unplug and mixing mechanism. Our industrial partner, ISS, further modified our design for easy manufacturing reason and fabricated the HPOC which made SMA actuator mixing test under pressure possible. A complete testing of the new HPOC system to observe bio-reagent mixing and reaction under high pressure was conducted and the results were satisfactory.

A Component-Wise Approach to Analyse a Composite Launcher Structure Subjected to Loading Factor

2016 ◽  
Author(s):  
Tommaso Cavallo ◽  
Alfonso Pagani ◽  
Enrico Zappino ◽  
Erasmo Carrera
Keyword(s):  
Composite Structures ◽  
Computational Cost ◽  
Free Vibration Analysis ◽  
High Strength ◽  
3D Models ◽  
Advanced Materials ◽  
Space Structures ◽  
One Dimensional ◽  
Computational Costs ◽  
The One

The space structures are realized by combining skin and reinforced components, such as longitudinal reinforcements called stringers and transversal reinforcements called ribs. These reinforced structures allow two main design requirements to be satisfied, the former is the light weight and the latter is a high strength. Solid models (3D) are widely used in the Finite Element Method (FEM) to analyse space structures because they have a high accuracy, in contrast they also have a high number of degrees of freedoms (DOFs) and huge computational costs. For these reasons the one-dimensional models (1D) are gaining success as alternative to 3D models. Classical models, such as Euler-Bernoulli or Timoshenko beam theories, allow the computational cost to be reduced but they are limited by their assumptions. Different refined models have been proposed to overcome these limitations and to extend the use of 1D models to the analysis of complex geometries or advanced materials. In this work very complex space structures are analyzed using 1D model based on the Carrera Unified Formulation (CUF). The free-vibration analysis of isotropic and composite structures are shown. The effects of the loading factor on the natural frequencies of an outline of launcher similar to the Arian V have been investigated. The results highlight the capability of the present refined one-dimensional model to reduce the computational costs without reducing the accuracy of the analysis.

scholarly journals Study of one-dimensional cure simulation applicable conditions for thick laminates and its comparison with three-dimensional simulation

2018 ◽  
Vol 25 (6) ◽  
pp. 1197-1204 ◽  
Author(s):  
Mingfa Ren ◽  
Qi Wang ◽  
Jie Cong ◽  
Xin Chang
Keyword(s):  
Computational Cost ◽  
Three Dimensional ◽  
Cure Kinetics ◽  
Transient Heat Conduction ◽  
Material System ◽  
Element Analysis ◽  
One Dimensional ◽  
Dimensional Simulation ◽  
The One ◽  
Three Dimensional Finite Element

AbstractThe comparison of one- and three-dimensional cure simulation of thick thermoset matrix laminates was conducted in this study. The applicable conditions of one-dimensional cure simulation were investigated. The transient heat conduction equation coupled to the cure kinetics was solved numerically using one- and three-dimensional finite element analysis. The evolution of temperature and degree of cure of the laminates during the curing process obtained by the simulation agreed well with the published experimental results. The results indicate that a wider one-dimensional analysis applicable region around the center point will be obtained in the laminate with a higher span-to-thickness ratio and in a less anisotropic material system. In the applicable region, the accuracy of the one-dimensional cure simulation can satisfy the engineering request and save the computational cost. While beyond the region, there is a steep increase in deviation of the one- and three-dimensional simulation results.

Characterisation of protein structure/function relationship by sequence analysis without previous alignment: Distinction between sub-groups of protein kinases

1995 ◽  
Vol 15 (3) ◽  
pp. 161-171 ◽  
Author(s):  
Marie-Anne Guerrucci ◽  
Robert Bellé
Keyword(s):  
Structure Function ◽  
Protein Kinases ◽  
Tyrosine Kinases ◽  
Large Scale ◽  
Data Bank ◽  
Structure Function Relationship ◽  
Protein Functions ◽  
Function Relationship ◽  
Related Proteins ◽  
Relationship Of

Using an approach for protein comparison by computer analysis based on signal treatment methods without previous alignment of the sequence, we have analysed the structure/function relationship of related proteins. The aim was to demonstrate that from a few members of related proteins, specific parameters can be obtained and used for the characterisation of newly sequenced proteins obtained by molecular biology techniques. The analysis was performed on protein kinases, which comprise the largest known family of proteins, and therefore allows valid estimations to be made. We show that using only a dozen defined proteins, the specific parameters extracted from their sequences classified the protein kinase family into two sub-groups: the protein serine/threonine kinases (PSKs) and the protein tyrosine kinases (PTKs). The analysis, largely involving computation, appears applicable to large scale data-bank analysis and prediction of protein functions.

scholarly journals Joint Angles and Mutual Coupling Estimation Algorithm for Bistatic MIMO Radar

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Jianfeng Li ◽  
Xiaofei Zhang
Keyword(s):  
Mutual Coupling ◽  
Multiple Input Multiple Output ◽  
Computational Cost ◽  
Estimation Algorithm ◽  
Mimo Radar ◽  
Coupling Coefficients ◽  
Angle Estimation ◽  
One Dimensional ◽  
Input Multiple Output ◽  
The One

We study the problem of angle estimation for a bistatic multiple-input multiple-output (MIMO) radar with unknown mutual coupling and proposed a joint algorithm for angles and mutual coupling estimation with the characteristics of uniform linear arrays and subspaces exploitation. We primarily obtain an initial estimate of DOA and DOD, then employ the local one-dimensional searching to estimate exactly DOA and DOD, and finally evaluate the parameters of mutual coupling coefficients via the estimated angles. Exploiting twice of the one-dimensional local searching, our method has much lower computational cost than the algorithm in (Liu and Liao (2012)), and automatically obtains the paired two-dimensional angle estimation. Slightly better performance for angle estimation has been achieved via our scheme in contrast to (Liu and Liao (2012)), while the two methods indicate very close performance of mutual coupling estimation. The simulation results verify the algorithmic effectiveness of our scheme.

scholarly journals GEODYNAMICS

GEODYNAMICS ◽  
2011 ◽  
Vol 2(11)2011 (2(11)) ◽  
pp. 155-157
Author(s):  
B. Ladanivskyy ◽  
◽  
Keyword(s):  
Transfer Function ◽  
Field Source ◽  
One Dimensional ◽  
Conductivity Model ◽  
The Earth ◽  
Mantle Conductivity ◽  
The One ◽  
Relationship Of ◽  
The Relationship ◽  
Source Structure

The regional magneto-variational sounding method (aka Z/H method) was used for estimation of the Earth's mantle conductivity model at the Panagurishte (PAG) observatory region. A magneto-variational transfer function is calculated on the base of the relationship of vertical to horizontal geomagnetic field spectra components recorded on the Earth surface and priori assumptions about a field source structure. Inversions of the transfer function allow to obtain the one dimensional conductivity model.

scholarly journals Reduction of radiation biases by incorporating the missing cloud variability via downscaling techniques: a study using the 3-D MoCaRT model

2012 ◽  
Vol 5 (1) ◽  
pp. 1543-1573
Author(s):  
S. Gimeno García ◽  
T. Trautmann ◽  
V. Venema
Keyword(s):  
Radiative Transfer ◽  
Spatial Resolution ◽  
Heterogeneous Media ◽  
Climate Modeling ◽  
Computational Cost ◽  
Three Dimensional ◽  
Accurate Solution ◽  
Stochastic Methods ◽  
One Dimensional ◽  
The One

Abstract. To handle complexity to the smallest detail in atmospheric radiative transfer models is in practice unfeasible. On the one hand, the properties of the interacting medium, i.e. the atmosphere and the surface, are only available at a limited spatial resolution. On the other hand, the computational cost of accurate radiation models accounting for three-dimensional heterogeneous media are prohibitive for some applications, esp. for climate modeling and operational remote sensing algorithms. Hence, it is still common practice to use simplified models for atmospheric radiation applications. Three-dimensional radiation models can deal with much more complexity than the one-dimensional ones providing a more accurate solution of the radiative transfer. In turn, one-dimensional models introduce biases to the radiation results. With the help of stochastic models that consider the multi-fractal nature of clouds, it is possible to scale cloud properties given at a coarse spatial resolution down to a finer resolution. Performing the radiative transfer within the spatially fine-resolved cloud fields noticeably helps to improve the radiation results. In the framework of this paper, we aim at characterizing cloud heterogeneity effects on radiances and broadband flux densities, namely: the errors due to unresolved variability (the so-called plane parallel homogeneous, PPH, bias) and the errors due to the neglect of transversal photon displacements (independent pixel approximation, IPA, bias). First, we study the effect of the missing cloud variability on reflectivities. We will show that the generation of subscale variability by means of stochastic methods greatly reduce or nearly eliminate the reflectivity biases. Secondly, three-dimensional broadband flux densities in the presence of realistic inhomogeneous cloud fields sampled at fine spatial resolutions are calculated and compared to their one-dimensional counterparts at coarser resolutions.

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