The Experts below are selected from a list of 64374 Experts worldwide ranked by ideXlab platform
Peter G Bolhuis - One of the best experts on this subject based on the ideXlab platform.
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approximating free energy and committor landscapes in standard transition path sampling using Virtual Interface exchange
Journal of Chemical Physics, 2019Co-Authors: Faidon Z Brotzakis, Peter G BolhuisAbstract:Transition path sampling is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of transition path sampling does not directly provide the free energy landscape nor the kinetics. This drawback has motivated the development of path sampling extensions able to simultaneously access both kinetics and thermodynamics, such as transition Interface sampling, and the reweighted path ensemble. However, performing transition Interface sampling is more involved than standard two-state transition path sampling and still requires (some) insight into the reaction to define Interfaces. While packages that can efficiently compute path ensembles for transition Interface sampling are now available, it would be useful to directly compute the free energy from a single standard transition path sampling simulation. To achieve this, we present here an approximate method, denoted Virtual Interface exchange transition path sampling, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a standard single transition path sampling simulation, as well as enables a committor analysis.
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approximating free energy and committor landscapes in standard transition path sampling using Virtual Interface exchange
arXiv: Chemical Physics, 2019Co-Authors: Faidon Z Brotzakis, Peter G BolhuisAbstract:Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not directly provide the free energy landscape nor the kinetics, which motivated the development of path sampling extensions, such as transition Interface sampling (TIS), and the reweighted paths ensemble (RPE), that are able to simultaneously access both kinetics and thermodynamics. However, performing TIS is more involved than TPS, and still requires (some) insight in the reaction to define Interfaces. While packages that can efficiently compute path ensembles for TIS are now available, it would be useful to directly compute the free energy from a single TPS simulation. To achieve this, we developed an approximate method, denoted Virtual Interface Exchange, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a single TPS, as well as enables a full committor analysis.
Sungin Jung - One of the best experts on this subject based on the ideXlab platform.
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design and implementation of a user level sockets layer over Virtual Interface architecture
Concurrency and Computation: Practice and Experience, 2003Co-Authors: Sungin Jung, Soonhoi HaAbstract:SUMMARY The Virtual Interface Architecture (VIA) is an industrystandard user-level communication architecture for system area networks. The VIA provides a protected, directly-accessible Interface to a network hardware, removing the operating system from the critical communication path. In this paper, we design and implement a user-level Sockets layer over VIA, named SOVIA (Sockets Over VIA). Our objective is to use the SOVIA layer to accelerate the existing Sockets-based applications with a reasonable effort and to provide a portable and high-performance communication library based on VIA to application developers. SOVIA realizes comparable performance to native VIA, showing a minimum one-way latency of 10.5 µs and a peak bandwidth of 814 Mbps on Giganet’s cLAN. We have shown the functional compatibility with the existing Sockets API by porting File Transfer Protocol (FTP) and Remote Procedure Call (RPC) applications over the SOVIA layer. Compared to the Giganet’s LAN Emulation (LANE) driver which emulates TCP/IP inside the kernel, SOVIA easily doubles the file transfer bandwidth in FTP and reduces the latency of calling an empty remote procedure by 77% in RPC applications. Copyright c � 2003 John Wiley & Sons, Ltd.
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gnbd via a network block device over Virtual Interface architecture on linux
International Parallel and Distributed Processing Symposium, 2002Co-Authors: Sungin JungAbstract:This paper describes a design and implementation of GNBD/VIA, a network block device (NBD) over Virtual Interface architecture (VIA), and evaluates its performance on Linux-based cluster of PCs. VIA is a user-level memory-mapped communication model which provides zero-copy communication by removing the operating system from the critical communication path. Typically, an NBD layer offers the abstraction of a storage media across the network. GNBD/VIA attempts to improve the performance of the NBD layer by employing the lightweight VIA communication mechanisms between NBD servers and clients. To our best knowledge, GNBD/VIA is the first implementation of NBD on VIA. GNBD/VIA outperforms the normal NBD placed on top of TCP/IP protocol stacks, and achieves the performance comparable to local disk devices, showing the read (write) bandwidth of 30.6MB/s (25.9MB/s) on the evaluation platform with UDM.9100 hard disks and Emulex cLAN adapters.
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IPDPS - GNBD/VIA: a network block device over Virtual Interface architecture on Linux
Proceedings 16th International Parallel and Distributed Processing Symposium, 2002Co-Authors: Kang-ho Kim, Jin-soo Kim, Sungin JungAbstract:This paper describes a design and implementation of GNBD/VIA, a network block device (NBD) over Virtual Interface architecture (VIA), and evaluates its performance on Linux-based cluster of PCs. VIA is a user-level memory-mapped communication model which provides zero-copy communication by removing the operating system from the critical communication path. Typically, an NBD layer offers the abstraction of a storage media across the network. GNBD/VIA attempts to improve the performance of the NBD layer by employing the lightweight VIA communication mechanisms between NBD servers and clients. To our best knowledge, GNBD/VIA is the first implementation of NBD on VIA. GNBD/VIA outperforms the normal NBD placed on top of TCP/IP protocol stacks, and achieves the performance comparable to local disk devices, showing the read (write) bandwidth of 30.6MB/s (25.9MB/s) on the evaluation platform with UDM.9100 hard disks and Emulex cLAN adapters.
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sovia a user level sockets layer over Virtual Interface architecture
Foundations of Computer Science, 2001Co-Authors: Sungin JungAbstract:The Virtual Interface Architecture (VIA) is an industry standard user-level communication architecture for system area networks. The VIA provides a protected, directly-accessible Interface to a network hardware, removing the operating system from the critical communication path. In this paper, we design and implement a user-level Sockets layer over VIA, named SOVIA (Sockets Over VIA). Our objective is to use the SOVIA layer to accelerate the existing Sockets-based applications with a reasonable effort and to provide a portable and high performance communication library based on VIA to the application developers.SOVIA realizes comparable performance to native VIA, showing the minimum latency of 10.5usec and the peak bandwidth of 814Mbps on Giganet's cLAN. We have verified the functional compatibility with the existing Sockets API by porting FTP (File Transfer Protocol) and RPC (Remote Procedure Call) applications over the SOVIA layer. Compared to the Giganet's LANE driver which emulates TCP/IP inside the kernel, SOVIA easily doubles the file transfer bandwidth in FTP and reduces the latency of calling an empty remote procedure by 77% in RPC applications.
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CLUSTER - SOVIA: a user-level sockets layer over Virtual Interface architecture
Proceedings 2001 IEEE International Conference on Cluster Computing, 2001Co-Authors: Jin-soo Kim, Kang-ho Kim, Sungin JungAbstract:The Virtual Interface Architecture (VIA) is an industry standard user-level communication architecture for system area networks. The VIA provides a protected, directly-accessible Interface to a network hardware, removing the operating system from the critical communication path. In this paper, we design and implement a user-level Sockets layer over VIA, named SOVIA (Sockets Over VIA). Our objective is to use the SOVIA layer to accelerate the existing Sockets-based applications with a reasonable effort and to provide a portable and high performance communication library based on VIA to the application developers.SOVIA realizes comparable performance to native VIA, showing the minimum latency of 10.5usec and the peak bandwidth of 814Mbps on Giganet's cLAN. We have verified the functional compatibility with the existing Sockets API by porting FTP (File Transfer Protocol) and RPC (Remote Procedure Call) applications over the SOVIA layer. Compared to the Giganet's LANE driver which emulates TCP/IP inside the kernel, SOVIA easily doubles the file transfer bandwidth in FTP and reduces the latency of calling an empty remote procedure by 77% in RPC applications.
Faidon Z Brotzakis - One of the best experts on this subject based on the ideXlab platform.
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approximating free energy and committor landscapes in standard transition path sampling using Virtual Interface exchange
Journal of Chemical Physics, 2019Co-Authors: Faidon Z Brotzakis, Peter G BolhuisAbstract:Transition path sampling is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of transition path sampling does not directly provide the free energy landscape nor the kinetics. This drawback has motivated the development of path sampling extensions able to simultaneously access both kinetics and thermodynamics, such as transition Interface sampling, and the reweighted path ensemble. However, performing transition Interface sampling is more involved than standard two-state transition path sampling and still requires (some) insight into the reaction to define Interfaces. While packages that can efficiently compute path ensembles for transition Interface sampling are now available, it would be useful to directly compute the free energy from a single standard transition path sampling simulation. To achieve this, we present here an approximate method, denoted Virtual Interface exchange transition path sampling, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a standard single transition path sampling simulation, as well as enables a committor analysis.
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approximating free energy and committor landscapes in standard transition path sampling using Virtual Interface exchange
arXiv: Chemical Physics, 2019Co-Authors: Faidon Z Brotzakis, Peter G BolhuisAbstract:Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not directly provide the free energy landscape nor the kinetics, which motivated the development of path sampling extensions, such as transition Interface sampling (TIS), and the reweighted paths ensemble (RPE), that are able to simultaneously access both kinetics and thermodynamics. However, performing TIS is more involved than TPS, and still requires (some) insight in the reaction to define Interfaces. While packages that can efficiently compute path ensembles for TIS are now available, it would be useful to directly compute the free energy from a single TPS simulation. To achieve this, we developed an approximate method, denoted Virtual Interface Exchange, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a single TPS, as well as enables a full committor analysis.
Nikolas J. Podraza - One of the best experts on this subject based on the ideXlab platform.
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Optical gradients in a-Si:H thin films detected using real-time spectroscopic ellipsometry with Virtual Interface analysis
Applied Surface Science, 2018Co-Authors: Maxwell M. Junda, Laxmi Karki Gautam, Robert W. Collins, Nikolas J. PodrazaAbstract:Abstract Virtual Interface analysis (VIA) is applied to real time spectroscopic ellipsometry measurements taken during the growth of hydrogenated amorphous silicon (a-Si:H) thin films using various hydrogen dilutions of precursor gases and on different substrates during plasma enhanced chemical vapor deposition. A procedure is developed for optimizing VIA model configurations by adjusting sampling depth into the film and the analyzed spectral range such that model fits with the lowest possible error function are achieved. The optimal VIA configurations are found to be different depending on hydrogen dilution, substrate composition, and instantaneous film thickness. A depth profile in the optical properties of the films is then extracted that results from a variation in an optical absorption broadening parameter in a parametric a-Si:H model as a function of film thickness during deposition. Previously identified relationships are used linking this broadening parameter to the overall shape of the optical properties. This parameter is observed to converge after about 2000–3000 A of accumulated thickness in all layers, implying that similar order in the a-Si:H network can be reached after sufficient thicknesses. In the early stages of growth, however, significant variations in broadening resulting from substrate- and processing-induced order are detected and tracked as a function of bulk layer thickness yielding an optical property depth profile in the final film. The best results are achieved with the simplest film-on-substrate structures while limitations are identified in cases where films have been deposited on more complex substrate structures.
Jin-soo Kim - One of the best experts on this subject based on the ideXlab platform.
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IPDPS - GNBD/VIA: a network block device over Virtual Interface architecture on Linux
Proceedings 16th International Parallel and Distributed Processing Symposium, 2002Co-Authors: Kang-ho Kim, Jin-soo Kim, Sungin JungAbstract:This paper describes a design and implementation of GNBD/VIA, a network block device (NBD) over Virtual Interface architecture (VIA), and evaluates its performance on Linux-based cluster of PCs. VIA is a user-level memory-mapped communication model which provides zero-copy communication by removing the operating system from the critical communication path. Typically, an NBD layer offers the abstraction of a storage media across the network. GNBD/VIA attempts to improve the performance of the NBD layer by employing the lightweight VIA communication mechanisms between NBD servers and clients. To our best knowledge, GNBD/VIA is the first implementation of NBD on VIA. GNBD/VIA outperforms the normal NBD placed on top of TCP/IP protocol stacks, and achieves the performance comparable to local disk devices, showing the read (write) bandwidth of 30.6MB/s (25.9MB/s) on the evaluation platform with UDM.9100 hard disks and Emulex cLAN adapters.
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CLUSTER - SOVIA: a user-level sockets layer over Virtual Interface architecture
Proceedings 2001 IEEE International Conference on Cluster Computing, 2001Co-Authors: Jin-soo Kim, Kang-ho Kim, Sungin JungAbstract:The Virtual Interface Architecture (VIA) is an industry standard user-level communication architecture for system area networks. The VIA provides a protected, directly-accessible Interface to a network hardware, removing the operating system from the critical communication path. In this paper, we design and implement a user-level Sockets layer over VIA, named SOVIA (Sockets Over VIA). Our objective is to use the SOVIA layer to accelerate the existing Sockets-based applications with a reasonable effort and to provide a portable and high performance communication library based on VIA to the application developers.SOVIA realizes comparable performance to native VIA, showing the minimum latency of 10.5usec and the peak bandwidth of 814Mbps on Giganet's cLAN. We have verified the functional compatibility with the existing Sockets API by porting FTP (File Transfer Protocol) and RPC (Remote Procedure Call) applications over the SOVIA layer. Compared to the Giganet's LANE driver which emulates TCP/IP inside the kernel, SOVIA easily doubles the file transfer bandwidth in FTP and reduces the latency of calling an empty remote procedure by 77% in RPC applications.
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ICS - Building a high-performance communication layer over Virtual Interface architecture on Linux clusters
Proceedings of the 15th international conference on Supercomputing - ICS '01, 2001Co-Authors: Jin-soo Kim, Kang-ho Kim, Sungin JungAbstract:The Virtual Interface Architecture (VIA) is an industry standard user-level communication architecture for cluster or system area networks. The VIA provides a protected, directly-accessible Interface to a network hardware, removing the operating system from the critical communication path. Although the VIA enables low-latency high-bandwidth communication, the application programming Interface defined in the VIA specification lacks many high-level features. In this paper, we develop a high performance communication layer over VIA, named SOVIA (Sockets Over VIA). Our goal is to make the SOVIA layer as efficient as possible so that the performance of native VIA can be delivered to the application, while retaining the portable Sockets semantics. We find that the single-threaded implementation with conditional sender-side buffering is effective in reducing latency. To increase bandwidth, we implement a flow control mechanism similar to the TCP's sliding window protocol. Our flow control mechanism is enhanced further by adding delayed acknowledgments and the ability to combine small messages. With these optimizations, SOVIA realizes comparable performance to native VIA, showing the latency of 10.5 µsec for 4-byte messages and the peak bandwidth of 814Mbps on Giganet's cLAN. The functional validity of SOVIA is verified by porting FTP (File Transfer Protocol) application over SOVIA.
