Programmable Function Research Articles

(Identity-based) dual receiver encryption from lattice-based programmable hash functions with high min-entropy

Dual receiver encryption (DRE) is an important cryptographic primitive introduced by Diament et al. at CCS’04, which allows two independent receivers to decrypt a same ciphertext to obtain the same plaintext. This primitive is quite useful in designing combined public key cryptosystems and denial of service attack-resilient protocols. In this paper, we obtain some results as follows. Using weak lattice-based programmable hash functions (wLPHF) with high min-entropy (Crypto’16), we give a generic IND-CCA secure DRE construction in the standard model. Furthermore, we get a concrete DRE scheme by instantiating a concrete wLPHF with high min-entropy.For DRE notion in the identity-based setting, identity-based DRE (IB-DRE), basing on lattice-based programmable hash functions (LPHF) with high min-entropy, we give a framework of IND-ID-CPA secure IB-DRE construction in the standard model. When instantiating with concrete LPHFs with high min-entropy, we obtain five concrete IB-DRE schemes.

Biomedical Applications of DNA-Based Molecular Devices.

Strict Watson-Crick base pairing and availability by automated synthesis have allowed deoxyribonucleic acid (DNA) molecules to be used as engineerable building blocks for constructing versatile nanostructures. In recent decades, with the development of DNA nanotechnology, a range of DNA-based dynamic molecular devices with sophisticated nanostructures have been designed and constructed. Featuring programmability and biocompatibility, the applications of DNA-based nanodevices have been extensively focused on the interfaces of biological systems. This review summarizes the recent progress in the design of DNA devices exhibiting programmable functions for biomedical applications. In vitro and in vivo applications of DNA-based nanodevices in cellular imaging and systemic drug delivery are highlighted. The challenges and open opportunities are also discussed.

Two‐step, piecewise‐linear SAR ADC with programmable transfer function

A 7-bit successive approximation register (SAR) analogue-to-digital converter (ADC) with programmable transfer functions is presented. Building upon prior art, a two-step successive approximation technique is used to implement a piecewise-linear approximation of the desired transfer function. However, unlike previous implementations of SAR-based non-linear ADCs, the proposed work demonstrates programmability of arbitrary non-linear transfer functions, thus making it suitable for a wide range of low-bandwidth applications. Simulation results from a proof-of-concept design in a standard 180 nm CMOS process are presented to validate the proposed idea.

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator.

To build complex genetic networks with predictable behaviors, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterization experiments and computational models for gene regulatory parts operating in isolation are routinely used to predict the dynamics of interconnected parts and guide the construction of new synthetic devices. Here, we individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and clustered regularly interspaced short palindromic repeats interference (CRISPRi), and show how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. We use a cell-free transcription-translation system (TXTL) to rapidly characterize the system, and we apply Bayesian inference to extract kinetic parameters for an ordinary differential equation-based mechanistic model. We then demonstrate in simulation and verify with TXTL experiments that the simultaneous regulation of a single gene target with STARs and CRISPRi leads to a pulse of gene expression. Our results suggest the modularity of the two regulators in an integrated genetic circuit, and we anticipate that construction and modeling frameworks that can leverage this modularity will become increasingly important as synthetic circuits increase in complexity.

Deterministic Identity-Based Encryption from Lattice-Based Programmable Hash Functions with High Min-Entropy

There only exists one deterministic identity-based encryption (DIBE) scheme which is adaptively secure in the auxiliary-input setting, under the learning with errors (LWE) assumption. However, the master public key consists of O(λ) basic matrices. In this paper, we consider to construct adaptively secure DIBE schemes with more compact public parameters from the LWE problem. (i) On the one hand, we gave a generic DIBE construction from lattice-based programmable hash functions with high min-entropy. (ii) On the other hand, when instantiating our generic DIBE construction with four LPHFs with high min-entropy, we can get four adaptively secure DIBE schemes with more compact public parameters. In one of our DIBE schemes, the master public key only consists of ω(log⁡λ) basic matrices.

Riboregulated toehold-gated gRNA for programmable CRISPR-Cas9 function.

Predictable control over gene expression is essential to elicit desired synthetic cellular phenotypes. Although CRISPR-Cas9 offers a simple RNA-guided method for targeted transcriptional control, it lacks the ability to integrate endogenous cellular information for efficient signal processing. Here, we present a new class of riboregulators termed toehold-gated gRNA (thgRNA) by integrating toehold riboswitches into sgRNA scaffolds, and demonstrate their programmability for multiplexed regulation in Escherichia coli with minimal cross-talks.

Rationally Designed DNA‐Origami Nanomaterials for Drug Delivery In Vivo

The recent decades have seen a surge of new nanomaterials designed for efficient drug delivery. DNA nanotechnology has been developed to construct sophisticated 3D nanostructures and artificial molecular devices that can be operated at the nanoscale, giving rise to a variety of programmable functions and fascinating applications. In particular, DNA-origami nanostructures feature rationally designed geometries and precise spatial addressability, as well as marked biocompatibility, thus providing a promising candidate for drug delivery. Here, the recent successful efforts to employ self-assembled DNA-origami nanostructures as drug-delivery vehicles are summarized. The remaining challenges and open opportunities are also discussed.

InKeV

InKeV is a network virtualization platform based on eBPF, an in-kernel execution engine recently upstreamed into linux kernel. InKeV's key contribution is that it enables in-kernel programmability and configuration of virtualized network functions, allowing to create a distributed virtual network across all edges hosting tenant workloads. Despite high performance demands of production environments, existing virtualization solutions have largely static in-kernel components due to the difficulty of developing and maintaining kernel modules and their years-long feature delivery time. The resulting compromise is either in programmability of network functions that rely on the data plane, such as payload processing, or in performance, due to expensive user-/kernel-space context switching. InKeV addresses these concerns: The use of eBPF allows it to dynamically insert programmable network functions into a running kernel, requiring neither to package a custom-kernel nor to hope for acceptance in mainline kernel. Its novel stitching feature allows to flexibly configure complete virtual networks by creating a graph of network functions inside the kernel. Our evaluation reports on the flexibility of InKeV, and in-kernel implementation benefits such as low-latency and impressive flow creation rate.

Engineering bacterial motility towards hydrogen-peroxide.

Synthetic biologists construct innovative genetic/biological systems to treat environmental, energy, and health problems. Many systems employ rewired cells for non-native product synthesis, while a few have employed the rewired cells as ‘smart’ devices with programmable function. Building on the latter, we developed a genetic construct to control and direct bacterial motility towards hydrogen peroxide, one of the body’s immune response signaling molecules. A motivation for this work is the creation of cells that can target and autonomously treat disease, the latter signaled by hydrogen peroxide release. Bacteria naturally move towards a variety of molecular cues (e.g., nutrients) in the process of chemotaxis. In this work, we engineered bacteria to recognize and move towards hydrogen peroxide, a non-native chemoattractant and potential toxin. Our system exploits oxyRS, the native oxidative stress regulon of E. coli. We first demonstrated H2O2-mediated upregulation motility regulator, CheZ. Using transwell assays, we showed a two-fold increase in net motility towards H2O2. Then, using a 2D cell tracking system, we quantified bacterial motility descriptors including velocity, % running (of tumble/run motions), and a dynamic net directionality towards the molecular cue. In CheZ mutants, we found that increased H2O2 concentration (0–200 μM) and induction time resulted in increased running speeds, ultimately reaching the native E. coli wild-type speed of ~22 μm/s with a ~45–65% ratio of running to tumbling. Finally, using a microfluidic device with stable H2O2 gradients, we characterized responses and the potential for “programmed” directionality towards H2O2 in quiescent fluids. Overall, the synthetic biology framework and tracking analysis in this work will provide a framework for investigating controlled motility of E. coli and other ‘smart’ probiotics for signal-directed treatment.

Relaxing state-access constraints in stateful programmable data planes

Supporting programmable stateful packet forwarding functions in hardware requires a tight balance between functionality and performance. Current state-of-the-art solutions are based on a very conservative model that assumes worst-case workloads. This finally limits the programmability of the system, even if actual deployment conditions may be very different from the worst-case scenario. We use trace-based simulations to highlight the benefits of accounting for specific workload characteristics. Furthermore, we show that relatively simple additions to a switching chip design can take advantage of such characteristics. In particular, we argue that introducing stalls in the switching chip pipeline enables stateful functions to be executed in a larger but bounded time without harming the overall forwarding performance. Our results show that, in some cases, the stateful processing of a packet could use 30x the time budget provided by state of the art solutions.

CHIMERA: A Field-Programmable Mixed-Signal IC With Time-Domain Configurable Analog Blocks

This paper presents a field-programmable mixed-signal IC named CHIMERA, for low-cost and rapid prototyping of mixed-signal systems. The proposed IC implements field-programmable analog functions with time-domain configurable analog blocks (TCABs). A single TCAB can be programmed to various analog circuits, including a time-to-digital converter, digitally-controlled oscillator, digitally-controlled delay cell, digital pulse-width modulator, and phase interpolator. The TCABs convey and process analog information using the frequency, pulse width, delay, or phase of digital pulses or pulse sequences, rather than using analog voltage or current signals for reduced susceptibility to attenuation and noise. The overall CHIMERA chip also includes arrays of configurable logic blocks (CLBs) and programmable arithmetic logic units (ALUs) for programmable digital functions. By programming the functionality of the TCAB, CLB, and ALU arrays and configuring the interconnects, the chip can implement various mixed-signal systems. A prototype IC fabricated with 65-nm CMOS technology demonstrates the versatile programmability of CHIMERA by being successfully operated as a 1-GHz phase-locked loop with a 12.3-psrms integrated jitter, as a 50-MS/s analog-to-digital converter with a 32.5-dB SNDR, and as a 1.2-to-0.7 V DC–DC converter with 95.5% efficiency.

A 37- $\mu \text{W}$ , Binary-Weighted PGA Based on a Novel Degeneration Transistor-Ladder

A programmable-gain amplifier with low power consumption is presented. The programmable gain function is achieved by varying the effective transconductance ratios of input and output stages, which is realized through innovative binary-weighted and triode-region transistor ladder. The proposed technique effectively overcomes the problems associated with the implementation of resistors ladder in these types of structures. The operational principle of this unique structure is discussed, its most important formulas are derived, and its outstanding performance is verified by post-layout simulations in TSMC 0.18- $\mu$ m N-well CMOS fabrication process. Owing to its unique construction, the proposed circuit combines the ever interesting constant bandwidth, linear-in-decibel, and fine-step programmable gain range merits all in a simple and low power structure. The core of proposed structure draws only 36.5 $\mu$ W from 1.8-V power supply. The circuit is capable of delivering a wide programmable range of about 37 dB and operating at frequencies up to 20 MHz. To approve the robustness of the structure, full process, voltage, and temperature variation analysis of the circuit is investigated through corner case and Monte Carlo simulations. Monte Carlo simulations show standard deviation values of less than 0.21 $\mu$ W and 0.5 dB in power consumption and voltage gain, respectively. These results indicate that the proposed structure would lend itself well for use in applications that demand high ratios of frequency over power consumption.

Homomorphic signatures with sublinear public keys via asymmetric programmable hash functions

We introduce the notion of asymmetric programmable hash functions (APHFs, for short), which adapts Programmable hash functions, introduced by Hofheinz and Kiltz (Crypto 2008, Springer, 2008), with two main differences. First, an APHF works over bilinear groups, and it is asymmetric in the sense that, while only secretly computable, it admits an isomorphic copy which is publicly computable. Second, in addition to the usual programmability, APHFs may have an alternative property that we call programmable pseudorandomness. In a nutshell, this property states that it is possible to embed a pseudorandom value as part of the function’s output, akin to a random oracle. In spite of the apparent limitation of being only secretly computable, APHFs turn out to be surprisingly powerful objects. We show that they can be used to generically implement both regular and linearly-homomorphic signature schemes in a simple and elegant way. More importantly, when instantiating these generic constructions with our concrete realizations of APHFs, we obtain: (1) the first linearly-homomorphic signature (in the standard model) whose public key is sub-linear in both the dataset size and the dimension of the signed vectors; (2) short signatures (in the standard model) whose public key is shorter than those by Hofheinz–Jager–Kiltz (Asiacrypt 2011, Springer, 2011) and essentially the same as those by Yamada et al. (CT-RSA 2012, Springer, 2012).

Binary control of enzymatic cleavage of DNA origami by structural antideterminants.

Controlling DNA nanostructure interaction with protein is essential in developing nanodevices with programmable function, reactivity, and stability for biological and medical applications. Here, we show that the sequence-specific action of restriction endonucleases towards sharp triangular or rectangular DNA origami exhibits a novel, binary ‘on/off’ behaviour, as canonical recognition sites are either essentially fully reactive, or strongly resistant to enzymatic cutting. Moreover, introduction of structural defects in the sharp triangle can activate an otherwise unreactive site, with a site-to-defect distance of ∼50 nm. We argue that site reactivity is dependent upon programmable, mechanical coupling in the two-dimensional DNA origami, with specific structural elements, including DNA nicks and branches proximal to the sites that can function as negative(anti) determinants of reactivity. Empirically modelling the constraints to DNA degrees of freedom associated with each recognition site in the sharp triangle can rationalize the pattern of suppressed reactivity towards nine restriction endonucleases, in substantial agreement with the experimental results. These results provide a basis for a predictive understanding of structure-reactivity correlates of specific DNA nanostructures, which will allow a better understanding of the behaviour of nucleic acids under nanoscale confinement, as well as in the rational design of functional nanodevices based on self-assembling nucleic acids.

Thermomechanically Tunable Elastic Metamaterials With Compliant Porous Structures

Adding programmable function to elastic metamaterials makes them versatile and intelligent. The objective of this study is to design and demonstrate thermomechanically tunable metamaterials with a compliant porous structure (CPS) and to analyze their thermomechanical behaviors. CPS, the unit cell of the metamaterial, is composed of rectangular holes, slits, and bimaterial hinges. By decomposing kinematic rotation of a linked arm and elastic deformation of a bimaterial hinge, a thermomechanical constitutive model of CPS is constructed, and the constitutive model is extended to a three-dimensional (3D) polyhedron structure for securing isotropic thermal properties. Temperature-dependent properties of base materials are implemented to the analytical model. The analytical model is verified with finite element (FE) based numerical simulations. A controllable range of temperature and strain is identified that is associated with a thermal deformation of the bimaterial hinge and contact on the slit surfaces of CPS. We also investigate the effect of geometry of CPS on the thermal expansion and effective stiffness of the metamaterial. The metamaterial with CPS has multiple transformation modes in response to temperature while keeping the same mechanical properties at room temperature, such as effective moduli and Poisson’s ratios. This work will pave the road toward the design of programmable metamaterials with both mechanically and thermally tunable capability, providing unique thermomechanical properties with a programmable function.

Design of a new CMOS Low-Power Analogue Neuron

In this paper, a low-power analogue complementary metal oxide semiconductor (CMOS) artificial neuron circuit is presented. The analogue neuron is composed of multiplier and programmable activation function circuits. The proposed four-quadrant multiplier has a single ended current output which eliminates the extra summation circuit at the output of the neuron that reduces the chip area as well as power consumption. In addition, programmability of activation function improves the neural network design process while enables the proposed neuron circuit to be used properly in learning algorithms such as back propagation. The most important feature of the proposed circuit is low power consumption and simple circuit topology. The performance of the circuit is confirmed by HSPICE simulations using 0.18 μm CMOS technology parameters. The circuit operates at 1 V supply voltage and consumes only 15 μW. Finally, different neural networks are realized using the proposed neuron circuit, which are successfully used to solve exclusive OR (XOR) problem and region classification problem to verify the accuracy and performance of the proposed circuit.

The Laser Control System for a Calibration Facility of a Light-Based Detector

Laser calibration facilities play a key role in the study and characterization of detectors like electromagnetic or hadronic calorimeters. They can be operated both during physics data taking and off runs. Typically, these facilities are based on a laser source which delivers light to each detector element via a light distribution system. The laser control (LC) system typically manages the interface between the experiment and the laser source, allowing the generation of light pulses according to specific needs such as detector calibration, study of detector performance in running conditions, and evaluation of data acquisition performance. Any specific implementation depends on hardware features. As an example, light pulses could be generated according to a physics distribution during physics runs or real data taking. In this case, light pulses should be generated according to a pattern that follows a programmable function and changes on a statistical base event by event. In this paper, we present a LC system for calibration of a calorimeter. It is a custom solution based on a hybrid platform hosting a field-programmable gate array and an ARM processor. We present the system architecture and the performances of a preliminary implementation. This system, in a more specific and specialized version, will be used in the Muon g-2 experiment (E989) at Fermilab.

Application of genome engineering in medical synthetic biology

Synthetic biology aims to establish a complete set of engineering principles, theories, and methods, via the rational design and assembly of basic biological parts, for the goal of effective implementation of complex biological systems with programmable functions. In recent years, with emerging novel classes of programmable genetic parts, in particular, the establishment and optimization of CRISPR and CRISPRi technology platforms, synthetic biology is entering a new era. This review summarizes recent advances on CRISPR genome editing and gene regulation technologies, their applications in constructing programmable biological parts, and their roles in building sophisticated gene circuits. We also provide a future vision on how synthetic biology can transform medicine (named medical synthetic biology, MSB) and therapeutics.

A low-power, fully programmable membership function generator using both transconductance and current modes

In this paper, a membership function generator (MFG) is presented which can produce triangular, trapezoidal, S-shaped or Z-shaped membership functions. The presented structure can operate in both trans-conductance (voltage–current) and current mode (current–current) with high programmability. The slope (keeping the height or width of the membership function constant), height (keeping the width constant) and width (keeping the height constant) of the membership function are independently programmable. Moreover, the width of the trapezoid can be varied without changing slope or height and all the generated shapes can be positioned horizontally. The topology, primarily, is presented in transconductance mode which can be converted to current mode with a little change in the input section of the circuit. Simulation results for the proposed circuit are presented in two operation modes. The most remarkable feature of the proposed MFG is its capability of generating outputs while consumes a very low amount of power. The analytical analysis of the proposed circuits is also given in HSPICE using TSMC 0.18 μm CMOS technology.

Magnetic nanoparticles meet microfluidics

Lab-on-a-chip immunoassays utilizing superparamagnetic beads as labels allowing for transport, separation and detection of different bead species. Technically, this is realized by employing magnetic strayfield landscapes and/or special channel geometries in microfluidic systems in combination with integrated magnetoresistive sensors. Moreover, the formation on magnetic bead superstructures due to dipolar magnetic interactions can be applied as configurable matter. This matter allows implementing programmable microfluidic functions such as mixers, filters or valves, which are able to simultaneously detect biomolecules via molecular recognition. This review focusses on physical aspects regarding the interaction of magnetic particles or magnetic bead superstructures in microfluidic environments. We will cover different transport as well as sensing concepts, which play an important role on the way to magnetically controlled lab–on-a-chip structures. Moreover, the realization of giant magnetoresistive sensors based on these magnetic bead superstructures will be discussed in detail.