The partition of the Mobile Phone Network (MPN) service area into the cell towers' Voronoi po... more The partition of the Mobile Phone Network (MPN) service area into the cell towers' Voronoi polygons (VP) may serve as a coordinate system for representing the location of the mobile phone devices. This view is shared by numerous papers that exploit mobile phone data for studying human spatial mobility. We investigate the credibility of this view by comparing volunteers' locational data of two kinds: (1) Cell towers' that served volunteers' connections and (2) The GPS tracks of the users at the time of connection. In more than 60\% of connections, user's mobile device was found outside the VP of the cell tower that served for the connection. We demonstrate that the area of possible device's location is many times larger than the area of the cell tower's VP. To comprise 90\% of the possible locations of the devices that may be connected to the cell tower one has to consider the tower's VP together with the two rings of the VPs adjacent to the tower'...
The partition of the Mobile Phone Network (MPN) service area into the cell towers’ Voronoi polygo... more The partition of the Mobile Phone Network (MPN) service area into the cell towers’ Voronoi polygons (VP) may serve as a coordinate system for representing the location of the mobile phone devices. This view is shared by numerous papers that exploit mobile phone data for studying human spatial mobility. We investigate the credibility of this view by comparing volunteers’ locational data of two kinds: (1) Cell towers’ that served volunteers’ connections and (2) The GPS tracks of the users at the time of connection. In more than 60% of connections, user’s mobile device was found outside the VP of the cell tower that served for the connection. We demonstrate that the area of possible device’s location is many times larger than the area of the cell tower’s VP. To comprise 90% of the possible locations of the devices that may be connected to the cell tower one has to consider the tower’s VP together with the two rings of the VPs adjacent to the tower’s VPs. An additional, third, ring of t...
Polymers is a class of molecules which can have many different structures due to a large number o... more Polymers is a class of molecules which can have many different structures due to a large number of degrees of freedom. Many biopolymers, e.g. DNA, but also synthetic macromolecules have special str ...
In this paper a stepwise compaction process of a ring semi-stiff polymer chain placed in a 3d con... more In this paper a stepwise compaction process of a ring semi-stiff polymer chain placed in a 3d conical nano-cavity and being under the action of the increasing external field is studied. Compaction ...
Sweden has adopted far less restrictive social distancing policies than most countries following ... more Sweden has adopted far less restrictive social distancing policies than most countries following the COVID-19 pandemic. This paper uses data on all mobile phone users, from one major Swedish mobile phone network, to examine the impact of the Coronavirus outbreak under the Swedish mild recommendations and restrictions regime on individual mobility and if changes in geographical mobility vary over different socio-economic strata. Having access to data for January-March in both 2019 and 2020 enables the estimation of causal effects of the COVID-19 outbreak by adopting a Difference-in-Differences research design. The paper reaches four main conclusions: (i) The daytime population in residential areas increased significantly (64 percent average increase); (ii) The daytime presence in industrial and commercial areas decreased significantly (33 percent average decrease); (iii) The distance individuals move from their homes during a day was substantially reduced (38 percent decrease in the ...
Polymers is a class of molecules which can have many different structures due to a large number o... more Polymers is a class of molecules which can have many different structures due to a large number of degrees of freedom. Many biopolymers, e.g. DNA, but also synthetic macromolecules have special structural features due to their backbone stiffness. Since such structural properties are important for e.g. the biological function, a lot of effort has been put into the investigation of the configurational properties of semi-stiff molecules. A theoretical treatment of these systems is often accompanied by computer simulations. The main idea is to compare theoretically derived models with experimental results for real polymers. Using Monte Carlo simulations, I have investigated how this computational technique can build a bridge between theoretical models and experimentally observed phenomena. The effort was mainly directed to develop sampling techniques, for efficiently exploring the configurational space of semi-stiff chains in a wide range of structures. The work was concentrated on comp...
GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to t... more GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.
Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier tha... more Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes cause the response to interploidy hybridizations, revealing an epigenetic basis of this phenomenon. In this study, we present evidence that paternal hypomethylation can bypass the interploidy hybridization barrier by alleviating the requirement for the Polycomb Repressive Complex 2 (PRC2) in the endosperm. PRC2 epigenetically regulates gene expression by applying methylation marks on histone H3. Bypass of the barrier is mediated by suppressed expression of imprinted genes. We show that the hypomethylated pollen genome causes de novo CHG methylation directed to FIS-PRC2 target genes, suggesting that different epigenetic modifications can functionally substitute for each other. Our work presents a method for the generation of viable triploids, providing an impressive example of the potential of epigenome manipul...
A semi-stiff charged polymer with counterions and salt was investigated using a Monte Carlo metho... more A semi-stiff charged polymer with counterions and salt was investigated using a Monte Carlo method with the Wang-Landau sampling scheme. Simulations show the coexistence of thermodynamically stable structures-prolonged and compact (toroidal-like). The transition between the two states is accompanied by concentration fluctuations for the condensing agent. Compact structures are accompanied by more multivalent counterions than prolonged ones.
The sampling of compact configurations is crucial when investigating structural properties of sem... more The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.
The conformational properties of charge-balanced polyampholytes described by the end-to-end dista... more The conformational properties of charge-balanced polyampholytes described by the end-to-end distance or radius of gyration depend on parameters such as the temperature and pH as well as on the detailed charge distribution along the backbone. In this work we present a method to determine the charge distribution along a semi-stiff polyampholyte backbone which will result in a thermodynamically stable structure for the compactness of interest, from several loops to an uncoiled structure, performed in a single computer experiment.
ABSTRACT New types of nanostructures are constantly being developed synthetically but are also fo... more ABSTRACT New types of nanostructures are constantly being developed synthetically but are also found in biological systems. Specific examples include the production of carbon nanocones as well as the conical core in some viruses. Such conical structures can be used to investigate the role of non-uniform confinement on the stability of e.g. toroidal structures formed by semi-stiff circular polymers, such as DNA. In this communication we are interested in the principal features of the compaction process. Using an external field and a conical confinement we observe several distinct shape transitions from a circle-like shape to several toroidal-like loops for both a two-dimensional and a three-dimensional system. The thermodynamic stability of these toroidal-like structures was investigated by evaluating their relative free energies using Monte Carlo simulations in the Extended Ensemble in the case of a two-dimensional system and by observing a hysteresis of the compaction-extension curve for the three-dimensional case.
The partition of the Mobile Phone Network (MPN) service area into the cell towers' Voronoi po... more The partition of the Mobile Phone Network (MPN) service area into the cell towers' Voronoi polygons (VP) may serve as a coordinate system for representing the location of the mobile phone devices. This view is shared by numerous papers that exploit mobile phone data for studying human spatial mobility. We investigate the credibility of this view by comparing volunteers' locational data of two kinds: (1) Cell towers' that served volunteers' connections and (2) The GPS tracks of the users at the time of connection. In more than 60\% of connections, user's mobile device was found outside the VP of the cell tower that served for the connection. We demonstrate that the area of possible device's location is many times larger than the area of the cell tower's VP. To comprise 90\% of the possible locations of the devices that may be connected to the cell tower one has to consider the tower's VP together with the two rings of the VPs adjacent to the tower'...
The partition of the Mobile Phone Network (MPN) service area into the cell towers’ Voronoi polygo... more The partition of the Mobile Phone Network (MPN) service area into the cell towers’ Voronoi polygons (VP) may serve as a coordinate system for representing the location of the mobile phone devices. This view is shared by numerous papers that exploit mobile phone data for studying human spatial mobility. We investigate the credibility of this view by comparing volunteers’ locational data of two kinds: (1) Cell towers’ that served volunteers’ connections and (2) The GPS tracks of the users at the time of connection. In more than 60% of connections, user’s mobile device was found outside the VP of the cell tower that served for the connection. We demonstrate that the area of possible device’s location is many times larger than the area of the cell tower’s VP. To comprise 90% of the possible locations of the devices that may be connected to the cell tower one has to consider the tower’s VP together with the two rings of the VPs adjacent to the tower’s VPs. An additional, third, ring of t...
Polymers is a class of molecules which can have many different structures due to a large number o... more Polymers is a class of molecules which can have many different structures due to a large number of degrees of freedom. Many biopolymers, e.g. DNA, but also synthetic macromolecules have special str ...
In this paper a stepwise compaction process of a ring semi-stiff polymer chain placed in a 3d con... more In this paper a stepwise compaction process of a ring semi-stiff polymer chain placed in a 3d conical nano-cavity and being under the action of the increasing external field is studied. Compaction ...
Sweden has adopted far less restrictive social distancing policies than most countries following ... more Sweden has adopted far less restrictive social distancing policies than most countries following the COVID-19 pandemic. This paper uses data on all mobile phone users, from one major Swedish mobile phone network, to examine the impact of the Coronavirus outbreak under the Swedish mild recommendations and restrictions regime on individual mobility and if changes in geographical mobility vary over different socio-economic strata. Having access to data for January-March in both 2019 and 2020 enables the estimation of causal effects of the COVID-19 outbreak by adopting a Difference-in-Differences research design. The paper reaches four main conclusions: (i) The daytime population in residential areas increased significantly (64 percent average increase); (ii) The daytime presence in industrial and commercial areas decreased significantly (33 percent average decrease); (iii) The distance individuals move from their homes during a day was substantially reduced (38 percent decrease in the ...
Polymers is a class of molecules which can have many different structures due to a large number o... more Polymers is a class of molecules which can have many different structures due to a large number of degrees of freedom. Many biopolymers, e.g. DNA, but also synthetic macromolecules have special structural features due to their backbone stiffness. Since such structural properties are important for e.g. the biological function, a lot of effort has been put into the investigation of the configurational properties of semi-stiff molecules. A theoretical treatment of these systems is often accompanied by computer simulations. The main idea is to compare theoretically derived models with experimental results for real polymers. Using Monte Carlo simulations, I have investigated how this computational technique can build a bridge between theoretical models and experimentally observed phenomena. The effort was mainly directed to develop sampling techniques, for efficiently exploring the configurational space of semi-stiff chains in a wide range of structures. The work was concentrated on comp...
GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to t... more GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.
Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier tha... more Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes cause the response to interploidy hybridizations, revealing an epigenetic basis of this phenomenon. In this study, we present evidence that paternal hypomethylation can bypass the interploidy hybridization barrier by alleviating the requirement for the Polycomb Repressive Complex 2 (PRC2) in the endosperm. PRC2 epigenetically regulates gene expression by applying methylation marks on histone H3. Bypass of the barrier is mediated by suppressed expression of imprinted genes. We show that the hypomethylated pollen genome causes de novo CHG methylation directed to FIS-PRC2 target genes, suggesting that different epigenetic modifications can functionally substitute for each other. Our work presents a method for the generation of viable triploids, providing an impressive example of the potential of epigenome manipul...
A semi-stiff charged polymer with counterions and salt was investigated using a Monte Carlo metho... more A semi-stiff charged polymer with counterions and salt was investigated using a Monte Carlo method with the Wang-Landau sampling scheme. Simulations show the coexistence of thermodynamically stable structures-prolonged and compact (toroidal-like). The transition between the two states is accompanied by concentration fluctuations for the condensing agent. Compact structures are accompanied by more multivalent counterions than prolonged ones.
The sampling of compact configurations is crucial when investigating structural properties of sem... more The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.
The conformational properties of charge-balanced polyampholytes described by the end-to-end dista... more The conformational properties of charge-balanced polyampholytes described by the end-to-end distance or radius of gyration depend on parameters such as the temperature and pH as well as on the detailed charge distribution along the backbone. In this work we present a method to determine the charge distribution along a semi-stiff polyampholyte backbone which will result in a thermodynamically stable structure for the compactness of interest, from several loops to an uncoiled structure, performed in a single computer experiment.
ABSTRACT New types of nanostructures are constantly being developed synthetically but are also fo... more ABSTRACT New types of nanostructures are constantly being developed synthetically but are also found in biological systems. Specific examples include the production of carbon nanocones as well as the conical core in some viruses. Such conical structures can be used to investigate the role of non-uniform confinement on the stability of e.g. toroidal structures formed by semi-stiff circular polymers, such as DNA. In this communication we are interested in the principal features of the compaction process. Using an external field and a conical confinement we observe several distinct shape transitions from a circle-like shape to several toroidal-like loops for both a two-dimensional and a three-dimensional system. The thermodynamic stability of these toroidal-like structures was investigated by evaluating their relative free energies using Monte Carlo simulations in the Extended Ensemble in the case of a two-dimensional system and by observing a hysteresis of the compaction-extension curve for the three-dimensional case.
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Papers by Alexey Siretskiy