Bayesian Optimization with Unknown Constraints

Recent work on Bayesian optimization has shown its effectiveness in global optimization of difficult black-box objective functions. Many real-world optimization problems of interest also have constraints which are unknown a priori. In this paper, we study Bayesian optimization for constrained problems in the general case that noise may be present in the constraint functions, and the objective and constraints may be evaluated independently. We provide motivating practical examples, and present a general framework to solve such problems. We demonstrate the effectiveness of our approach on optimizing the performance of online latent Dirichlet allocation subject to topic sparsity constraints, tuning a neural network given test-time memory constraints, and optimizing Hamiltonian Monte Carlo to achieve maximal effectiveness in a fixed time, subject to passing standard convergence diagnostics.Comment: 14 pages, 3 figure

Attraction Between Like-Charged Walls: Short-Ranged Simulations Using Local Molecular Field Theory

Effective attraction between like-charged walls mediated by counterions is studied using local molecular field (LMF) theory. Monte Carlo simulations of the "mimic system'' given by LMF theory, with short-ranged "Coulomb core" interactions in an effective single particle potential incorporating a mean-field average of the long-ranged Coulomb interactions, provide a direct test of the theory, and are in excellent agreement with more complex simulations of the full Coulomb system by Moreira and Netz [Eur. Phys. J. E 8, 33 (2002)]. A simple, generally-applicable criterion to determine the consistency parameter sigma_{min} needed for accurate use of the LMF theory is presented

Organized condensation of worm-like chains

We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a wrapping state is transformed into a complex multi-leafed, rosette structure as the adhesion energy is reduced. The statistical mechanics of the "melting" of a rosette can be mapped into an exactly soluble one-dimensional many-body problem.Comment: 15 pages, 2 figures in a pdf fil

Why is the condensed phase of DNA preferred at higher temperature? DNA compaction in the presence of a multivalent cation

Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation (spermine), at various temperatures and monovalent salt concentrations. We confirmed that the compact state is preferred at higher temperatures and at lower monovalent salt concentrations. This result is interpreted in terms of an increase in the net translational entropy of small ions due to ionic exchange between higher and lower valence ions.Comment: 4pages,3figure

Structural Polymorphism of the Cytoskeleton: A Model of Linker-Assisted Filament Aggregation

The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of linkers in the solution modifies the effective inter-rod interaction and can lead to inter-filament attraction. Depending on the system's composition and physical properties such as linker binding energies, filaments will either orient perpendicular or parallel to each other, leading to network-like or bundled structures. We show that such a system can have one of three generic phase diagrams, one dominated by bundles, another by networks, and the third containing both bundle and network-like phases. The first two diagrams can be found over a wide range of interaction energies, while the third occurs only for a narrow range. These results provide theoretical understanding of the classification of linker proteins as bundling proteins or crosslinking proteins. In addition, they suggest possible mechanisms by which the cell may control cytoskeletal morphology.Comment: 17 pages, 3 figure

Entropy-induced Microphase Separation in Hard Diblock Copolymers

Whereas entropy can induce phase behavior that is as rich as seen in energetic systems, microphase separation remains a very rare phenomenon in entropic systems. In this paper, we present a density functional approach to study the possibility of entropy-driven microphase separation in diblock copolymers. Our model system consists of copolymers composed of freely-jointed slender hard rods. The two types of monomeric segments have comparable lengths, but a significantly different diameter, the latter difference providing the driving force for the phase separation. At the same time these systems can also exhibit liquid crystalline phases. We treat this system in the appropriate generalization of the Onsager approximation to chain-like particles. Using a linear stability (bifurcation) analysis, we analytically determine the onset of the microseparated and the nematic phases for long chains. We find that for very long chains the microseparated phase always preempts the nematic. In the limit of infinitely long chains, the correlations within the chain become Gaussian and the approach becomes exact. This allows us to define a Gaussian limit in which the theory strongly simplifies and the competition between microphase separation and liquid crystal formation can be studied essentially analytically. Our main results are phase diagrams as a function of the effective diameter difference, the segment composition and the length ratio of the segments. We also determine the amplitude of the positional order as a function of position along the chain at the onset of the microphase separation instability. Finally, we give suggestions as to how this type of entropy-induced microphase separation could be observed experimentally.Comment: 16 pages, 7 figure

What do emulsification failure and Bose-Einstein condensation have in common?

Ideal bosons and classical ring polymers formed via self-assembly, are known to have the same partition function, and so analogous phase transitions. In ring polymers, the analogue of Bose-Einstein condensation occurs when a ring polymer of macroscopic size appears. We show that a transition of the same general form occurs within a whole class of systems with self-assembly, and illustrate it with the emulsification failure of a microemulsion phase of water, oil and surfactant. As with Bose-Einstein condensation, the transition occurs even in the absence of interactions.Comment: 7 pages, 1 figure, typeset with EUROTeX, uses epsfi

Torsional fluctuations in columnar DNA assemblies

In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy between neighbouring molecules explicitly depends on their relative azimuthal orientations. For DNA this leads to a rich variety of mesophases for columnar assemblies, each categorized by a specific azimuthal ordering. In a preceding paper [A. Wynveen, D. J. Lee, and A. A. Kornyshev, Eur. Phys. J. E, 16, 303 (2005)] a statistical mechanical theory was developed for the assemblies of torsionally rigid molecues in order to determine how thermal fluctuations influence the structure of these mesophases. Here we extend this theory by including torsional fluctuations of the molecules, where a DNA molecule may twist about its long axis at the cost of torsional elastic energy. Comparing this with the previous study, we find that inclusion of torsional fluctuations further increases the density at which the transition between the hexagonal structure and the predicted rhombic phase occurs and reduces the level of distortion in the rhombic phase. As X-ray diffraction may probe the 2-D lattice structure of such assemblies and provide information concerning the underlying interaction between molecules, we have also calculated correlation functions for the azimuthal ordering which are manifest in an x-ray scattering intensity profiles.Comment: 33 pages, 8 figure