A5056856569- Advanced Thermodynamics and Statistical Mechanics
- Plant Reproductive Biology
- Plant Molecular Biology Research
- Advanced Fluorescence Microscopy Techniques
- Protein Structure and Dynamics
- Quantum chaos and dynamical systems
- Spectroscopy and Quantum Chemical Studies
- Gene Regulatory Network Analysis
- ATP Synthase and ATPases Research
- Nonlinear Dynamics and Pattern Formation
- Advanced Chemical Physics Studies
- Polysaccharides and Plant Cell Walls
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Advanced Electron Microscopy Techniques and Applications
- Neural dynamics and brain function
- thermodynamics and calorimetric analyses
- Opinion Dynamics and Social Influence
- Advanced Biosensing Techniques and Applications
- Tree Root and Stability Studies
- Photosynthetic Processes and Mechanisms
- Complex Network Analysis Techniques
- Mitochondrial Function and Pathology
- Molecular spectroscopy and chirality
- Quantum, superfluid, helium dynamics
Stockholm University
2017-2024
Chengdu University of Traditional Chinese Medicine
2023
Hokkaido University
2007-2017
Sapporo Science Center
2017
Japan Science and Technology Agency
2005-2009
Centre de Recherche en Économie et Statistique
2009
Centre for Research in Engineering Surface Technology
2009
Center for Responsible Travel
2009
Lawrence Berkeley National Laboratory
2009
Kobe University
2005-2008
The shape and function of plant cells are often highly interdependent. puzzle-shaped that appear in the epidermis many plants a striking example complex cell shape, however their functional benefit has remained elusive. We propose these intricate forms provide an effective strategy to reduce mechanical stress wall epidermis. When tissue-level growth is isotropic, we hypothesize lobes emerge at cellular level prevent formation large isodiametric would bulge under produced by turgor pressure....
Conformational dynamics of proteins can be interpreted as itinerant motions the protein traverses from one state to another on a complex network in conformational space or, more generally, space. Here we present scheme extract multiscale (SSN) single-molecule time series. Analysis by this method enables us lift degeneracy--different physical states having same value for measured observable--as much possible. A or node is defined not observable at each but set subsequences over time. The...
We introduce a step transition and state identification (STaSI) method for piecewise constant single-molecule data with newly derived minimum description length equation as the objective function. detect transitions using Student's t test group segments into states by hierarchical clustering. The optimum number of is determined based on equation. This provides comprehensive, analysis multiple traces requiring few user inputs about underlying physical models faster more precise in determining...
No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used "configuration" TS pass only once, robustly exist up to a moderately high-energy regime above reaction threshold, even when nonlinear resonances among bath degrees of freedom perpendicular coordinate result local chaos. However, at much higher energy global chaos appears separability from starts lose locally. In space near saddles, it is found that slower system...
Using a single-molecule fluorescence approach, the time series of catalytic events an enzymatic reaction can be monitored, yielding sequence fluorescent "on"- and "off"-states. An accurate on/off-assignment is complicated by intrinsic extrinsic noise in every experiment. simulated data, performance most widely employed binning thresholding approach was systematically compared to change point analysis. It shown that underlying on- off-histograms as well off-autocorrelation are not necessarily...
Organ sizes and shapes are highly reproducible, or robust, within a species individuals. Arabidopsis thaliana sepals, which the leaf-like organs that enclose flower buds, have consistent size shape, indicating robust development. Cell growth is locally heterogeneous due to intrinsic extrinsic noise. To achieve organ fluctuations in cell must average an even rate requires uncorrelated anti-correlated time space. Here, we live image quantify development of sepals with increased decreased...
The reaction scheme of rotary catalysis and the torque generation mechanism bovine mitochondrial F 1 (bMF ) were studied in single-molecule experiments. Under ATP-saturated concentrations, high-speed imaging a single 40-nm gold bead attached to γ subunit bMF showed 2 types intervening pauses during rotation that discriminated by short dwell long dwell. Using ATPγS as slowly hydrolyzing ATP derivative well using functional mutant βE188D with slowed hydrolysis, pausing events distinctively...
Living tissues display fluctuations-random spatial and temporal variations of tissue properties around their reference values-at multiple scales. It is believed that such fluctuations may enable to sense state or size. Recent theoretical studies developed specific models in growing predicted growth show long-range correlations. Here, we elaborated upon these predictions tested them using experimental data. We first introduced a minimal model for the any quantity has some level persistence...
Organs form with remarkably consistent sizes and shapes during development, whereas a high variability in growth is observed at the cell level. Given this contrast, it unclear how such consistency organ scale can emerge from cellular behavior. Here, we examine an intermediate scale, of clones cells Arabidopsis sepals. Each clone consists progeny single progenitor cell. At early stages, find that derived small grow faster than those large This results reduction size variability, phenomenon...
A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes multiple pathways is presented employing principal component-based disconnectivity graphs Shannon entropy relative "sizes" superbasins. The incorporate a metric relationship between stationary points system, which enable us to capture not only actual assignment superbasins but also size each superbasin in configuration space. landscape measure quantifies degree topographical tells at regime...
A new method is presented to study bifurcation of no-return transition states (TSs) at potential saddles for systems many degrees freedom (dof). The enables us investigate analytically when and how the TS bifurcates. Our reveals a aspect dof, i.e., action variables bath dof play role control parameters as long they remain approximately conserved. As an illustrative example, we demonstrate our by using three atomic exchange reaction. TSs gives rise short-lived intermediate state saddle, which...
Abstract F 1 -ATPase (F ) is a rotary motor protein that can efficiently convert chemical energy to mechanical work of rotation via fine coordination its conformational motions and reaction sequences. Compared with reactant binding product release, the ATP hydrolysis has relatively little contributions torque generation. To scrutinize possible roles hydrolysis, we investigate detailed statistics catalytic dwells from high-speed single wild-type observations. Here report small during dwell...
By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations molecular motions associated with a straight-through tube in phase space inside which all reactive trajectories pass from one basin to another, eliminating recrossing configuration space. This visualization provides us intuition how species "walk along" reaction-rate slope multidimensional compared intrinsic path The distinct...
Statistics of the dwell times, stationary state distributions (SSDs), are often studied to infer underlying kinetics from a single molecule finite-level time series. However, it is well known that kinetic scheme, hidden Markov model (HMM), cannot be identified uniquely SSDs because some features HMM by measurements. Here, we quantify amount excessive information in given not warranted measured and extract with minimum as most objective representation data. The method applied enzymatic...
The fractional behavior is presented for a minimal Hamiltonian system of three degrees freedom which describes reaction processes. model has double-well potential where the Arnold web within well nonuniform. survival probability exhibits power law decay in addition to exponential decay. Moreover, trajectories exhibit 1/f spectra and subdiffusion action space, while show Lorentzian normal diffusion. Transient features these statistical properties reveal dynamical connection, i.e., how...
A new measure is presented to quantify the local topographical feature, i.e., diversity in transitions from a state others, on complex networks. This composed of two contributions: one related number outgoing links (known as degree) and other heterogeneity transition probabilities others associated with links. To illustrate potential measure, we apply it multiscale space networks (SSNs) extracted directly single-molecule time series protein fluctuation NADH:flavin oxidoreductase by using...
Reactivity boundaries that divide the origin and destination of trajectories are crucial importance to reveal mechanism reactions, which was recently found exist robustly even at high energies for index-one saddles [Phys. Rev. Lett. 105, 048304 (2010)]. Here we revisit concept reactivity boundary propose a more general definition can involve single reaction associated with bottleneck made up higher index and/or several saddle points different indices, where normal form theory, based on...
Single molecule fluorescence spectroscopy offers great potential for studying enzyme kinetics. A number of reporter systems allow monitoring the sequence individual reaction events with a confocal microscope. When using time-correlated single photon counting (TCSPC) detection scheme, additional information about lifetimes fluorophores can be obtained. We have applied TCSPC scheme kinetics α-chymotrypsin hydrolyzing double-substituted rhodamine 110-based fluorogenic substrate in two-step...
Abstract Characterization of states, the essential components underlying energy landscapes, is one most intriguing subjects in single-molecule (SM) experiments due to existence noise inherent measurements. Here we present a method extract state sequences from experimental SM time-series. Taking into account empirical error and finite sampling time-series, extracts steady-state network which provides an approximation effective free landscape. The core application rate-distortion theory...