Quorum sensing (QS) refers to the cell communication through signaling molecules that regulate many important biological functions of bacteria by monitoring their population density. Although a wide spectrum of studie...Quorum sensing (QS) refers to the cell communication through signaling molecules that regulate many important biological functions of bacteria by monitoring their population density. Although a wide spectrum of studies on the QS system mechanisms have been carried out in experiments, mathematical modeling to explore the QS system has become a powerful approach as well. In this paper, we review the research progress of network modeling in bacterial QS to capture the system's underlying mechanisms. There are four types of QS system models for bacteria: the Gram-negative QS system model, the Gram-positive QS system model, the model for both Gram-negative and Gram-positive QS system, and the synthetic QS system model. These QS system models are mostly described by the ordinary differential equations (ODE) or partial differential equations (PDE) to study the changes of signaling molecule dynamics in time and space and the cell population density variations. Besides the deterministic simulations, the stochastic modeling approaches have also been introduced to discuss the noise effects on kinetics in QS systems. Taken together, these current modeling efforts advance our understanding of the QS system by providing systematic and quantitative dynamics description, which can hardly be obtained in experiments.展开更多
Understanding the transport resistance of water molecules in polyamide(PA)reverse osmosis(RO)membranes at the molecular level is of great importance in guiding the design,preparation,and applications of these membrane...Understanding the transport resistance of water molecules in polyamide(PA)reverse osmosis(RO)membranes at the molecular level is of great importance in guiding the design,preparation,and applications of these membranes.In this work,we use molecular simulation to calculate the total transport resistance by dividing it into two contributions:the interior part and the interfacial part.The interior resistance is dependent on the thickness of the PA layer,while the interfacial resistance is not.Simulation based on the 5 nm PA layer reveals that interfacial resistance is the dominating contribution(>62%)to the total resistance.However,for real-world RO membranes with a 200 nm PA layer,interfacial resistance plays a minor role,with a contribution below 10%.This implies that there is a risk of inaccuracy when using the typical method to estimate the transport resistance of RO membranes,as this method involves simply multiplying the total transport resistance of the simulated value based on a membrane with a 5 nm PA layer.Furthermore,both the interfacial resistance and the interior resistance are dependent on the chemistry of the PA layer.Our simulation reveals that decreasing the number of residual carboxyl groups in the PA layer leads to decreased interior resistance;therefore,the water permeability can be improved at no cost of ion rejection,which is in excellent agreement with the experimental results.展开更多
In order to inhibit and remove the thin ice and extend the lifetime of the damaged bridge, the self-healing mechanism and hydrophobic performance of asphalt modified by siloxane and polyurethane (ASP) were studied by ...In order to inhibit and remove the thin ice and extend the lifetime of the damaged bridge, the self-healing mechanism and hydrophobic performance of asphalt modified by siloxane and polyurethane (ASP) were studied by dynamic shear rheology (DSR), fluorescence microscope (FM), atomic force microscope (AFM), the fracture-healing-re-fracture test and molecular simulations. The experimental results indicated that the selfhealing capability of ASP increased with increasing heating time and temperature. Furthermore, the addition of siloxane could improve the reaction energy barrier and complex modulus, and it is believed that the self-healing is a viscosity driven process, consisting of two parts namely crack closure and properties recovery. Contact angle of ASP increased with the increasing siloxane content and it deduced that the siloxane could improve the hydrophobic performance of ASP and the ASP molecule model could simulate well the self-healing mechanism and hydrophobic performance of ASP.展开更多
Major histocompatibility complex class I(MHC-I),a key element of the acquired immune system,plays essential roles in activating CD8^(+)T cells by recognizing intracellular antigens derived from pathogens and cancer.As...Major histocompatibility complex class I(MHC-I),a key element of the acquired immune system,plays essential roles in activating CD8^(+)T cells by recognizing intracellular antigens derived from pathogens and cancer.Assembly of MHC-I and antigen peptides is critical for the antigen presentation on the cell surface.However,the structural dynamics of antigenic peptide loading into MHC-I,at atomistic resolution,is still elusive.Here,by constructing a Markov state model(MSM)based onlarge scale all-atommolecular dynamics(MDs)simulations with an aggregated simulation time∼24μs,we reveal the detailed molecular mechanism underlying the peptide-loading dynamics into MHC-I and identify the key intermediates with associated thermodynamic/kinetic properties.Furthermore,we examine how the chaperone tapasin-binding protein related(TAPBPR)participates in promoting the peptide loading,and the results show that TAPBPR,by binding to the F pocket,allosterically modulates the structures of the distant pocket B,resulting in formation of a peptide-receptive conformation ideal for accommodating the incoming peptide N-terminus.This study provides fundamental structural insights for the peptide loading into MHC-I in both chaperone uncatalyzed and catalyzed contexts.展开更多
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11704318,11675134,and 11874310)the China Postdoctoral Science Foundation(Grant No.2016M602071).
文摘Quorum sensing (QS) refers to the cell communication through signaling molecules that regulate many important biological functions of bacteria by monitoring their population density. Although a wide spectrum of studies on the QS system mechanisms have been carried out in experiments, mathematical modeling to explore the QS system has become a powerful approach as well. In this paper, we review the research progress of network modeling in bacterial QS to capture the system's underlying mechanisms. There are four types of QS system models for bacteria: the Gram-negative QS system model, the Gram-positive QS system model, the model for both Gram-negative and Gram-positive QS system, and the synthetic QS system model. These QS system models are mostly described by the ordinary differential equations (ODE) or partial differential equations (PDE) to study the changes of signaling molecule dynamics in time and space and the cell population density variations. Besides the deterministic simulations, the stochastic modeling approaches have also been introduced to discuss the noise effects on kinetics in QS systems. Taken together, these current modeling efforts advance our understanding of the QS system by providing systematic and quantitative dynamics description, which can hardly be obtained in experiments.
基金Financial support from the National Key Research and Development Program of China(2017YFC0403902)the National Basic Research Program of China(2015CB655301)+5 种基金the National Natural Science Foundation of China(21825803)the Jiangsu Natural Science Foundations(BK20190085 and BK20150063)the Program of Excellent Innovation Teams of Jiangsu Higher Education Institutionsthe Project of Priority Academic Program Development of Jiangsu Higher Education Institutions is gratefully acknowledgedWe are also grateful to the High Performance Computing Center of Nanjing Tech Universitythe National Supercomputing Center in Wuxi for supporting us with computational resources.
文摘Understanding the transport resistance of water molecules in polyamide(PA)reverse osmosis(RO)membranes at the molecular level is of great importance in guiding the design,preparation,and applications of these membranes.In this work,we use molecular simulation to calculate the total transport resistance by dividing it into two contributions:the interior part and the interfacial part.The interior resistance is dependent on the thickness of the PA layer,while the interfacial resistance is not.Simulation based on the 5 nm PA layer reveals that interfacial resistance is the dominating contribution(>62%)to the total resistance.However,for real-world RO membranes with a 200 nm PA layer,interfacial resistance plays a minor role,with a contribution below 10%.This implies that there is a risk of inaccuracy when using the typical method to estimate the transport resistance of RO membranes,as this method involves simply multiplying the total transport resistance of the simulated value based on a membrane with a 5 nm PA layer.Furthermore,both the interfacial resistance and the interior resistance are dependent on the chemistry of the PA layer.Our simulation reveals that decreasing the number of residual carboxyl groups in the PA layer leads to decreased interior resistance;therefore,the water permeability can be improved at no cost of ion rejection,which is in excellent agreement with the experimental results.
基金Funded by the National Natural Science Foundation of China(No.51808329)Science and Technology Department of Shanxi Province International Cooperation(No.201603D421027)the Special Project of Commercialization of Shanxi Province Research Foundation(No.201804D131034)
文摘In order to inhibit and remove the thin ice and extend the lifetime of the damaged bridge, the self-healing mechanism and hydrophobic performance of asphalt modified by siloxane and polyurethane (ASP) were studied by dynamic shear rheology (DSR), fluorescence microscope (FM), atomic force microscope (AFM), the fracture-healing-re-fracture test and molecular simulations. The experimental results indicated that the selfhealing capability of ASP increased with increasing heating time and temperature. Furthermore, the addition of siloxane could improve the reaction energy barrier and complex modulus, and it is believed that the self-healing is a viscosity driven process, consisting of two parts namely crack closure and properties recovery. Contact angle of ASP increased with the increasing siloxane content and it deduced that the siloxane could improve the hydrophobic performance of ASP and the ASP molecule model could simulate well the self-healing mechanism and hydrophobic performance of ASP.
基金The authors acknowledge the Natural Science Foundation of Shanghai(nos.20511101900,20ZR1427200,and 20ZR1425400).
文摘Major histocompatibility complex class I(MHC-I),a key element of the acquired immune system,plays essential roles in activating CD8^(+)T cells by recognizing intracellular antigens derived from pathogens and cancer.Assembly of MHC-I and antigen peptides is critical for the antigen presentation on the cell surface.However,the structural dynamics of antigenic peptide loading into MHC-I,at atomistic resolution,is still elusive.Here,by constructing a Markov state model(MSM)based onlarge scale all-atommolecular dynamics(MDs)simulations with an aggregated simulation time∼24μs,we reveal the detailed molecular mechanism underlying the peptide-loading dynamics into MHC-I and identify the key intermediates with associated thermodynamic/kinetic properties.Furthermore,we examine how the chaperone tapasin-binding protein related(TAPBPR)participates in promoting the peptide loading,and the results show that TAPBPR,by binding to the F pocket,allosterically modulates the structures of the distant pocket B,resulting in formation of a peptide-receptive conformation ideal for accommodating the incoming peptide N-terminus.This study provides fundamental structural insights for the peptide loading into MHC-I in both chaperone uncatalyzed and catalyzed contexts.
