5,524 research outputs found
Designing algorithms to aid discovery by chemical robots
Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery
Accurate prediction of gene feedback circuit behavior from component properties
A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology
Enhanced many-body effects in the excitation spectrum of a weakly-interacting rotating Bose-Einstein condensate
The excitation spectrum of a highly-condensed two-dimensional trapped
Bose-Einstein condensate (BEC) is investigated within the rotating frame of
reference. The rotation is used to transfer high-lying excited states to the
low-energy spectrum of the BEC. We employ many-body linear-response theory and
show that, once the rotation leads to a quantized vortex in the ground state,
already the low-energy part of the excitation spectrum shows substantial
many-body effects beyond the realm of mean-field theory. We demonstrate
numerically that the many-body effects grow with the vorticity of the ground
state, meaning that the rotation enhances them even for very weak repulsion.
Furthermore, we explore the impact of the number of bosons in the
condensate on a low-lying single-particle excitation, which is describable
within mean-field theory. Our analysis shows deviations between the many-body
and mean-field results which clearly persist when is increased up to the
experimentally relevant regime, typically ranging from several thousand up to a
million bosons in size. Implications are briefly discussed
Linear Boolean classification, coding and "the critical problem"
The problem of constructing a minimal rank matrix over GF(2) whose kernel
does not intersect a given set S is considered. In the case where S is a
Hamming ball centered at 0, this is equivalent to finding linear codes of
largest dimension. For a general set, this is an instance of "the critical
problem" posed by Crapo and Rota in 1970. This work focuses on the case where S
is an annulus. As opposed to balls, it is shown that an optimal kernel is
composed not only of dense but also of sparse vectors, and the optimal mixture
is identified in various cases. These findings corroborate a proposed
conjecture that for annulus of inner and outer radius nq and np respectively,
the optimal relative rank is given by (1-q)H(p/(1-q)), an extension of the
Gilbert-Varshamov bound H(p) conjectured for Hamming balls of radius np
Time-dependent multi-orbital mean-field for fragmented Bose-Einstein condensates
The evolution of Bose-Einstein condensates is usually described by the famous
time-dependent Gross-Pitaevskii equation, which assumes all bosons to reside in
a single time-dependent orbital. In the present work we address the evolution
of fragmented condensates, for which two (or more) orbitals are occupied, and
derive a corresponding time-dependent multi-orbital mean-field theory. We call
our theory TDMF(), where stands for the number of evolving fragments.
Working equations for a general two-body interaction between the bosons are
explicitly presented along with an illustrative numerical example.Comment: 16 pages, 1 figur
Zoo of quantum phases and excitations of cold bosonic atoms in optical lattices
Quantum phases and phase transitions of weakly- to strongly-interacting
bosonic atoms in deep to shallow optical lattices are described by a {\it
single multi-orbital mean-field approach in real space}. For weakly-interacting
bosons in 1D, the critical value of the superfluid to Mott insulator (MI)
transition found is in excellent agreement with {\it many-body} treatments of
the Bose-Hubbard model. For strongly-interacting bosons, (i) additional MI
phases appear, for which two (or more) atoms residing in {\it each site}
undergo a Tonks-Girardeau-like transition and localize and (ii) on-site
excitation becomes the excitation lowest in energy. Experimental implications
are discussed.Comment: 12 pages, 3 figure
L-selectin mediated leukocyte tethering in shear flow is controlled by multiple contacts and cytoskeletal anchorage facilitating fast rebinding events
L-selectin mediated tethers result in leukocyte rolling only above a
threshold in shear. Here we present biophysical modeling based on recently
published data from flow chamber experiments (Dwir et al., J. Cell Biol. 163:
649-659, 2003) which supports the interpretation that L-selectin mediated
tethers below the shear threshold correspond to single L-selectin carbohydrate
bonds dissociating on the time scale of milliseconds, whereas L-selectin
mediated tethers above the shear threshold are stabilized by multiple bonds and
fast rebinding of broken bonds, resulting in tether lifetimes on the timescale
of seconds. Our calculations for cluster dissociation suggest that
the single molecule rebinding rate is of the order of Hz. A similar
estimate results if increased tether dissociation for tail-truncated L-selectin
mutants above the shear threshold is modeled as diffusive escape of single
receptors from the rebinding region due to increased mobility. Using computer
simulations, we show that our model yields first order dissociation kinetics
and exponential dependence of tether dissociation rates on shear stress. Our
results suggest that multiple contacts, cytoskeletal anchorage of L-selectin
and local rebinding of ligand play important roles in L-selectin tether
stabilization and progression of tethers into persistent rolling on endothelial
surfaces.Comment: 9 pages, Revtex, 4 Postscript figures include
Build-up of coherence between initially-independent subsystems: The case of Bose-Einstein condensates
When initially-independent subsystems are made to contact, {\it coherence}
can develop due to interaction between them. We exemplify and demonstrate this
paradigm through several scenarios of two initially-independent Bose-Einstein
condensates which are allowed to collide. The build-up of coherence depends
strongly on time, interaction strength and other parameters of each condensate.
Implications are discussed.Comment: 11 pages, 3 figure
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