@article{8385,
abstract = {We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver.},
author = {Sperl, Georg and Narain, Rahul and Wojtan, Christopher J},
issn = {1557-7368},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {Association for Computing Machinery},
title = {{Homogenized yarn-level cloth}},
doi = {10.1145/3386569.3392412},
volume = {39},
year = {2020},
}
@phdthesis{8386,
abstract = {Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical
quantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—
our design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints
were taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.},
author = {Zhang, Ran},
issn = {2663-337X},
pages = {148},
publisher = {Institute of Science and Technology Austria},
title = {{Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability}},
doi = {10.15479/AT:ISTA:8386},
year = {2020},
}
@phdthesis{8390,
abstract = {Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction
for tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually
dissimilar domains. },
author = {Royer, Amélie},
isbn = {978-3-99078-007-7},
issn = {2663-337X},
pages = {197},
publisher = {Institute of Science and Technology Austria},
title = {{Leveraging structure in Computer Vision tasks for flexible Deep Learning models}},
doi = {10.15479/AT:ISTA:8390},
year = {2020},
}
@article{8402,
abstract = {Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.
Results: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.
Conclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.},
author = {Rampelt, Heike and Sucec, Iva and Bersch, Beate and Horten, Patrick and Perschil, Inge and Martinou, Jean-Claude and van der Laan, Martin and Wiedemann, Nils and Schanda, Paul and Pfanner, Nikolaus},
issn = {1741-7007},
journal = {BMC Biology},
keywords = {Biotechnology, Plant Science, General Biochemistry, Genetics and Molecular Biology, Developmental Biology, Cell Biology, Physiology, Ecology, Evolution, Behavior and Systematics, Structural Biology, General Agricultural and Biological Sciences},
publisher = {Springer Nature},
title = {{The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments}},
doi = {10.1186/s12915-019-0733-6},
volume = {18},
year = {2020},
}
@unpublished{8403,
abstract = {Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding of how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity vs. specificity.},
author = {Sučec, Iva and Wang, Yong and Dakhlaoui, Ons and Weinhäupl, Katharina and Jores, Tobias and Costa, Doriane and Hessel, Audrey and Brennich, Martha and Rapaport, Doron and Lindorff-Larsen, Kresten and Bersch, Beate and Schanda, Paul},
booktitle = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
title = {{Structural basis of client specificity in mitochondrial membrane-protein chaperones}},
doi = {10.1101/2020.06.08.140772},
year = {2020},
}
@unpublished{8404,
abstract = {The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX3C-Xn-CX3C motifs are formed, short marginally stable α-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles.},
author = {Weinhäupl, Katharina and Wang, Yong and Hessel, Audrey and Brennich, Martha and Lindorff-Larsen, Kresten and Schanda, Paul},
booktitle = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
title = {{Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone}},
doi = {10.1101/2020.03.13.990150},
year = {2020},
}
@book{8414,
abstract = {Arnold diffusion, which concerns the appearance of chaos in classical mechanics, is one of the most important problems in the fields of dynamical systems and mathematical physics. Since it was discovered by Vladimir Arnold in 1963, it has attracted the efforts of some of the most prominent researchers in mathematics. The question is whether a typical perturbation of a particular system will result in chaotic or unstable dynamical phenomena. In this groundbreaking book, Vadim Kaloshin and Ke Zhang provide the first complete proof of Arnold diffusion, demonstrating that that there is topological instability for typical perturbations of five-dimensional integrable systems (two and a half degrees of freedom).
This proof realizes a plan John Mather announced in 2003 but was unable to complete before his death. Kaloshin and Zhang follow Mather’s strategy but emphasize a more Hamiltonian approach, tying together normal forms theory, hyperbolic theory, Mather theory, and weak KAM theory. Offering a complete, clean, and modern explanation of the steps involved in the proof, and a clear account of background material, this book is designed to be accessible to students as well as researchers. The result is a critical contribution to mathematical physics and dynamical systems, especially Hamiltonian systems.},
author = {Kaloshin, Vadim and Zhang, Ke},
isbn = {9-780-6912-0253-2},
pages = {224},
publisher = {Princeton University Press},
title = {{Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom}},
doi = {10.1515/9780691204932},
volume = {208},
year = {2020},
}
@inproceedings{8533,
abstract = {Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Jecker, Ismael R and Svoboda, Jakub},
booktitle = {45th International Symposium on Mathematical Foundations of Computer Science},
isbn = {9783959771597},
issn = {1868-8969},
location = {Prague, Czech Republic},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Simplified game of life: Algorithms and complexity}},
doi = {10.4230/LIPIcs.MFCS.2020.22},
volume = {170},
year = {2020},
}
@inproceedings{8534,
abstract = {A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.},
author = {Jecker, Ismael R and Kupferman, Orna and Mazzocchi, Nicolas},
booktitle = {45th International Symposium on Mathematical Foundations of Computer Science},
isbn = {9783959771597},
issn = {1868-8969},
location = {Prague, Czech Republic},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Unary prime languages}},
doi = {10.4230/LIPIcs.MFCS.2020.51},
volume = {170},
year = {2020},
}
@article{8535,
abstract = {We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.},
author = {Skrivan, Tomas and Soderstrom, Andreas and Johansson, John and Sprenger, Christoph and Museth, Ken and Wojtan, Christopher J},
issn = {1557-7368},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {Association for Computing Machinery},
title = {{Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces}},
doi = {10.1145/3386569.3392466},
volume = {39},
year = {2020},
}
@article{8562,
abstract = {Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.
However, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable
configurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface.},
author = {Gavriil, Konstantinos and Guseinov, Ruslan and Perez Rodriguez, Jesus and Pellis, Davide and Henderson, Paul M and Rist, Florian and Pottmann, Helmut and Bickel, Bernd},
issn = {1557-7368},
journal = {ACM Transactions on Graphics},
number = {6},
publisher = {Association for Computing Machinery},
title = {{Computational design of cold bent glass façades}},
doi = {10.1145/3414685.3417843},
volume = {39},
year = {2020},
}
@misc{8563,
abstract = {Supplementary data provided for the provided for the publication:
Igor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife.},
author = {Csicsvari, Jozsef L and Gridchyn, Igor and Schönenberger, Philipp},
publisher = {Institute of Science and Technology Austria},
title = {{Optogenetic alteration of hippocampal network activity}},
doi = {10.15479/AT:ISTA:8563},
year = {2020},
}
@article{8568,
abstract = {Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.},
author = {Prehal, Christian and Fitzek, Harald and Kothleitner, Gerald and Presser, Volker and Gollas, Bernhard and Freunberger, Stefan Alexander and Abbas, Qamar},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry},
publisher = {Springer Nature},
title = {{Persistent and reversible solid iodine electrodeposition in nanoporous carbons}},
doi = {10.1038/s41467-020-18610-6},
volume = {11},
year = {2020},
}
@inproceedings{8571,
abstract = {We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.},
author = {Geretti, Luca and Alexandre Dit Sandretto, Julien and Althoff, Matthias and Benet, Luis and Chapoutot, Alexandre and Chen, Xin and Collins, Pieter and Forets, Marcelo and Freire, Daniel and Immler, Fabian and Kochdumper, Niklas and Sanders, David and Schilling, Christian},
booktitle = {EPiC Series in Computing},
pages = {49--75},
publisher = {EasyChair},
title = {{ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics}},
doi = {10.29007/zkf6},
volume = {74},
year = {2020},
}
@inproceedings{8572,
abstract = {We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.},
author = {Althoff, Matthias and Bak, Stanley and Bao, Zongnan and Forets, Marcelo and Frehse, Goran and Freire, Daniel and Kochdumper, Niklas and Li, Yangge and Mitra, Sayan and Ray, Rajarshi and Schilling, Christian and Schupp, Stefan and Wetzlinger, Mark},
booktitle = {EPiC Series in Computing},
pages = {16--48},
publisher = {EasyChair},
title = {{ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics}},
doi = {10.29007/7dt2},
volume = {74},
year = {2020},
}
@phdthesis{8574,
abstract = {This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes
leave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation.
In Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful
tool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real
behavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.
In Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.
We give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both
drift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions.
In Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare
the results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction.
In the last chapter, we give a brief outlook to further research. },
author = {Szep, Eniko},
issn = {2663-337X},
pages = {158},
publisher = {Institute of Science and Technology Austria},
title = {{Local adaptation in metapopulations}},
doi = {10.15479/AT:ISTA:8574},
year = {2020},
}
@article{8579,
abstract = {Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.},
author = {Andrei, Andreea and Öztürk, Yavuz and Khalfaoui-Hassani, Bahia and Rauch, Juna and Marckmann, Dorian and Trasnea, Petru Iulian and Daldal, Fevzi and Koch, Hans-Georg},
issn = {2077-0375},
journal = {Membranes},
number = {9},
publisher = {MDPI},
title = {{Cu homeostasis in bacteria: The ins and outs}},
doi = {10.3390/membranes10090242},
volume = {10},
year = {2020},
}
@inproceedings{8580,
abstract = {We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.},
author = {Graff, Grzegorz and Graff, Beata and Jablonski, Grzegorz and Narkiewicz, Krzysztof},
booktitle = {11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, },
isbn = {9781728157511},
location = {Pisa, Italy},
publisher = {IEEE},
title = {{The application of persistent homology in the analysis of heart rate variability}},
doi = {10.1109/ESGCO49734.2020.9158054},
year = {2020},
}
@article{8581,
abstract = {The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.},
author = {Pinke, Gergely and Zhou, Long and Sazanov, Leonid A},
issn = {1545-9985},
journal = {Nature Structural and Molecular Biology},
number = {11},
pages = {1077--1085},
publisher = {Springer Nature},
title = {{Cryo-EM structure of the entire mammalian F-type ATP synthase}},
doi = {10.1038/s41594-020-0503-8},
volume = {27},
year = {2020},
}
@article{8587,
abstract = {Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules.},
author = {Li, Xiang and Yakaboylu, Enderalp and Bighin, Giacomo and Schmidt, Richard and Lemeshko, Mikhail and Deuchert, Andreas},
issn = {1089-7690},
journal = {The Journal of Chemical Physics},
keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy},
number = {16},
publisher = {AIP Publishing},
title = {{Intermolecular forces and correlations mediated by a phonon bath}},
doi = {10.1063/1.5144759},
volume = {152},
year = {2020},
}