Xinwei Shi | University of California, Davis (original) (raw)

Papers by Xinwei Shi

Electrostatics interactions play a major role in the stabilization of biomolecules: as such, they... more Electrostatics interactions play a major role in the stabilization of biomolecules: as such, they remain a major focus of theoretical and computational studies in biophysics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explicitly provide an accurate estimate of these interactions, they are usually computationally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on Poisson theory. The Poisson-Boltzmann equation (PBE) treats the system in a mean field approximation, providing reasonable estimates of electrostatics interactions in a solvent treated as continuum. In the first part of this paper, we review the theory behind the PBE, including recent improvement in which ions size and dipolar features of solvent molecules are taken into account explicitly. The PBE is a non linear second order differen...

Abstract. We present an approach to define and extract the cavities on the surfaces of macromolec... more Abstract. We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins. (a) (b) (c) Fig. 1. Two cavities on the surface of a Thrombin protein molecule. Figure (a) illustrates the cavities on the surface with different colors. The red curves are the boundaries of the cavities. Figure (b) and (c) illustrate the zoomed views of the two cavities. 1

Electrostatics interactions play a major role in the stabilization of biomolecules : as such, the... more Electrostatics interactions play a major role in the stabilization of biomolecules : as such, they remain a major focus of theoretical and computational studies in biophysics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explicitly provide an accurate estimate of these interactions, they are usually computationally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on Poisson theory. The PoissonBoltzmann equation (PBE) treats the system in a mean field approximation, providing reasonable estimates of electrostatics interactions in a solvent treated as continuum. In the first part of this paper, we review the theory behind the PBE, including recent improvement in which ions size and dipolar features of solvent molecules are taken into account explicitly. The PBE is a non linear second order differen...

Electrostaticsinteractionsplayamajorroleinthestabilizationofbiomolecules : as such, they remain a... more Electrostaticsinteractionsplayamajorroleinthestabilizationofbiomolecules : as such, they remain a major focus of theoretical and computational studies in bio- physics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explic- itly provide an accurate estimate of these interactions, they are usually computation- ally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on Poisson theory. The Poisson- Boltzmann equation (PBE) treats the system in a mean field approximation, providing reasonable estimates of electrostatics interactions in a solvent treated as continuum. In the first part of this paper, we review the theory behind the PBE, including recent improvement in which ions size and dipolar features of solvent molecules are taken into account explicitly. The PBE is a non linear second order differenti...

Computer Aided Geometric Design, 2011

Computational Geometry, 2009

We present an approach to define and extract the cavities on the surfaces of macromolecules. Each... more We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins.

JCI Insight

METHODS. A prototype algorithm, developed from first principles of electrostatic field theory, de... more METHODS. A prototype algorithm, developed from first principles of electrostatic field theory, derives charge density (CD) as a spatial representation of the true sources of the cardiac field. The algorithm processes multiple, simultaneous, noncontact voltage measurements within the cardiac chamber to inversely derive the global distribution of CD sources across the endocardial surface. RESULTS. Comparison of CD to an established computer-simulated model of atrial conduction demonstrated feasibility in terms of spatial, temporal, and morphologic metrics. Inverse reconstruction matched simulation with median spatial errors of 1.73 mm and 2.41 mm for CD and voltage, respectively. Median temporal error was less than 0.96 ms and morphologic correlation was greater than 0.90 for both CD and voltage. Activation patterns observed in human atrial flutter reproduced those established through contact maps, with a 4-fold improvement in resolution noted for CD over voltage. Global activation maps (charge density-based) are reported in atrial fibrillation with confirmed reduction of far-field interference. Arrhythmia cycle-length slowing and termination achieved through ablation of critical points demonstrated in the maps indicates both mechanistic and pathophysiological relevance. CONCLUSION. Global maps of cardiac activation based on CD enable classification of conduction patterns and localized nonpulmonary vein therapeutic targets in atrial fibrillation. The measurement capabilities of the approach have roles spanning deep phenotyping to therapeutic application. TRIAL REGISTRATION. ClinicalTrials.gov NCT01875614.

In this paper, we propose a new method for computing the geometric measures of bio-molecules usin... more In this paper, we propose a new method for computing the geometric measures of bio-molecules using skin surfaces to represent their shapes. Specifically, we give the formu- las for measuring the total area A and volume V of the skin surface defined by n weighted points, as well as the contributions of the individual points to A and V. Motivation.

Japanese Conference on Discrete and Computational Geometry, 2000

We present an approach to define and extract the cavities on the surfaces of macromolecules. Each... more We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a trian- gular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins.

Lecture Notes in Computer Science, 2006

ABSTRACT This paper presents an algorithm to generate quality tetrahedral meshes for the volumes ... more ABSTRACT This paper presents an algorithm to generate quality tetrahedral meshes for the volumes bounded by the molecular skin model defined by Edelsbrunner. The algorithm applies the Delaunay refinement to the tetrahedral meshes bounded by quality surface meshes. In particular, we iteratively insert the circumcenters of bad shape tetrahedra with a priority parameterized by its distance from the surface. We achieve a bounded radius-edge ratio for the tetrahedral mesh after the refinement. Finally, we apply the sliver exudation algorithm to remove ‘slivers’. The algorithm terminates with guarantees on the tetrahedral quality and an accurate approximation of the original surface boundary.

IEEE Visualization 2004, 2004

We present an approach to define and extract the cavities on the surfaces of macromolecules. Each... more We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins. (a) (b) (c) Fig. 1. Two cavities on the surface of a Thrombin protein molecule. Figure (a) illustrates the cavities on the surface with different colors. The red curves are the boundaries of the cavities. Figure (b) and (c) illustrate the zoomed views of the two cavities.

Electrostatics interactions play a major role in the stabilization of biomolecules: as such, they... more Electrostatics interactions play a major role in the stabilization of biomolecules: as such, they remain a major focus of theoretical and computational studies in biophysics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explicitly provide an accurate estimate of these interactions, they are usually computationally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on Poisson theory. The Poisson-Boltzmann equation (PBE) treats the system in a mean field approximation, providing reasonable estimates of electrostatics interactions in a solvent treated as continuum. In the first part of this paper, we review the theory behind the PBE, including recent improvement in which ions size and dipolar features of solvent molecules are taken into account explicitly. The PBE is a non linear second order differen...

Abstract. We present an approach to define and extract the cavities on the surfaces of macromolec... more Abstract. We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins. (a) (b) (c) Fig. 1. Two cavities on the surface of a Thrombin protein molecule. Figure (a) illustrates the cavities on the surface with different colors. The red curves are the boundaries of the cavities. Figure (b) and (c) illustrate the zoomed views of the two cavities. 1

Electrostatics interactions play a major role in the stabilization of biomolecules : as such, the... more Electrostatics interactions play a major role in the stabilization of biomolecules : as such, they remain a major focus of theoretical and computational studies in biophysics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explicitly provide an accurate estimate of these interactions, they are usually computationally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on Poisson theory. The PoissonBoltzmann equation (PBE) treats the system in a mean field approximation, providing reasonable estimates of electrostatics interactions in a solvent treated as continuum. In the first part of this paper, we review the theory behind the PBE, including recent improvement in which ions size and dipolar features of solvent molecules are taken into account explicitly. The PBE is a non linear second order differen...

Electrostaticsinteractionsplayamajorroleinthestabilizationofbiomolecules : as such, they remain a... more Electrostaticsinteractionsplayamajorroleinthestabilizationofbiomolecules : as such, they remain a major focus of theoretical and computational studies in bio- physics. Electrostatics in solution is strongly dependent on the nature of the solvent and on the ions it contains. While methods that treat the solvent and ions explic- itly provide an accurate estimate of these interactions, they are usually computation- ally too demanding to study large macromolecular systems. Implicit solvent methods provide a viable alternative, especially those based on Poisson theory. The Poisson- Boltzmann equation (PBE) treats the system in a mean field approximation, providing reasonable estimates of electrostatics interactions in a solvent treated as continuum. In the first part of this paper, we review the theory behind the PBE, including recent improvement in which ions size and dipolar features of solvent molecules are taken into account explicitly. The PBE is a non linear second order differenti...

Computer Aided Geometric Design, 2011

Computational Geometry, 2009

We present an approach to define and extract the cavities on the surfaces of macromolecules. Each... more We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins.

JCI Insight

METHODS. A prototype algorithm, developed from first principles of electrostatic field theory, de... more METHODS. A prototype algorithm, developed from first principles of electrostatic field theory, derives charge density (CD) as a spatial representation of the true sources of the cardiac field. The algorithm processes multiple, simultaneous, noncontact voltage measurements within the cardiac chamber to inversely derive the global distribution of CD sources across the endocardial surface. RESULTS. Comparison of CD to an established computer-simulated model of atrial conduction demonstrated feasibility in terms of spatial, temporal, and morphologic metrics. Inverse reconstruction matched simulation with median spatial errors of 1.73 mm and 2.41 mm for CD and voltage, respectively. Median temporal error was less than 0.96 ms and morphologic correlation was greater than 0.90 for both CD and voltage. Activation patterns observed in human atrial flutter reproduced those established through contact maps, with a 4-fold improvement in resolution noted for CD over voltage. Global activation maps (charge density-based) are reported in atrial fibrillation with confirmed reduction of far-field interference. Arrhythmia cycle-length slowing and termination achieved through ablation of critical points demonstrated in the maps indicates both mechanistic and pathophysiological relevance. CONCLUSION. Global maps of cardiac activation based on CD enable classification of conduction patterns and localized nonpulmonary vein therapeutic targets in atrial fibrillation. The measurement capabilities of the approach have roles spanning deep phenotyping to therapeutic application. TRIAL REGISTRATION. ClinicalTrials.gov NCT01875614.

In this paper, we propose a new method for computing the geometric measures of bio-molecules usin... more In this paper, we propose a new method for computing the geometric measures of bio-molecules using skin surfaces to represent their shapes. Specifically, we give the formu- las for measuring the total area A and volume V of the skin surface defined by n weighted points, as well as the contributions of the individual points to A and V. Motivation.

Japanese Conference on Discrete and Computational Geometry, 2000

We present an approach to define and extract the cavities on the surfaces of macromolecules. Each... more We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a trian- gular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins.

Lecture Notes in Computer Science, 2006

ABSTRACT This paper presents an algorithm to generate quality tetrahedral meshes for the volumes ... more ABSTRACT This paper presents an algorithm to generate quality tetrahedral meshes for the volumes bounded by the molecular skin model defined by Edelsbrunner. The algorithm applies the Delaunay refinement to the tetrahedral meshes bounded by quality surface meshes. In particular, we iteratively insert the circumcenters of bad shape tetrahedra with a priority parameterized by its distance from the surface. We achieve a bounded radius-edge ratio for the tetrahedral mesh after the refinement. Finally, we apply the sliver exudation algorithm to remove ‘slivers’. The algorithm terminates with guarantees on the tetrahedral quality and an accurate approximation of the original surface boundary.

IEEE Visualization 2004, 2004

We present an approach to define and extract the cavities on the surfaces of macromolecules. Each... more We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins. (a) (b) (c) Fig. 1. Two cavities on the surface of a Thrombin protein molecule. Figure (a) illustrates the cavities on the surface with different colors. The red curves are the boundaries of the cavities. Figure (b) and (c) illustrate the zoomed views of the two cavities.