За Розалинд Франклин и кристализирането на ДНК

Тъй като стигнахме до един много интересен етап на проекта при който накратко проучваме как да си направим кристалчета от ДНК, белтъци или РНК, попаднах на интересна информация за кристалографията и ми се ще да ви споделя някои забавни неща.

Всички днес знаем, че ДНК е двойна спирала. За откривателни на тази структура се смятат Джеймс Уотсън, Франсис Крик и Морис Уилкинс, които си спечелват световна слава и дори Нобелова награда. Откритията на една жена обаче се оказват ключови за техния успех, въпреки че Уотсън и Крик никога не го признават публично. Тази жена е Розалинд Фраклин, млада и амбициозна изследователка в King’s College London. Розалинд Франклин и нейния колега Морис Уилкинс целяли да получат възможно най-чисти кристали от ДНК, които да изследват чрез рентгенови лъчи и по получената дифракционна картина да установят каква е структурата на молекулата. В процеса на работа откриват, че ДНК съществува в две основни форми – в течна среда нишките ДНК са дълги и тънки, а в суха – скъсени и по-дебели, като нарекли двете форми съответно “В” и “А”. След всички многобройни проучвания, кристализации и кристалографии, през януари 1953 година Розалинд Франклин достигнала до идеята, че и двете форми имат спирална структура. Дотук добре, обаче как точно изглеждат тези спирали?

На 30 януари 1953 година в лабораторията на Франклин буквално връхлита Франсис Крик – учен от Кавендишката лаборатория в Кеймбридж, носейки грешното предположение за структурата на ДНК на Линус Полинг. Крик й предлага интересна оферта – да си сътрудничат и да публикуват верни резултати преди Линус Полинг да е осъзнал грешката си. Франклин притежавала снимката, а Крик – умението да я разчита. Обаче намекът на Крик, че Франклин не е способна сама да разчита информацията, която получава, силно я ядосал и тя незаинтересована отхвърлила предложението му. И тук в историята се включва предателят – Морис Уилкинс, който без знанието на Франклин показал на Крик известната снимка на ДНК номер 51, лично дело на Розалинд Франклин и неин помощник. Крик пък го запознал с грешните резултати на Линус Полинг. Така на 7 март 1953 година моделът на ДНК вече бил построен и в нито една от научните публикации на Уотсън и Крик няма дори да се спомене името на Розалинд Франклин, докато Уилкинс снизходително ще определя нейните изследвания като “доста полезни”. За откритието си тримата учени получават Нобелова награда през 1962 г., с което наистина настава нова ера в биологията.

Колкото до Розалинд Франклин…дали в резултат от продължителното облъчване от работата с рентгена или на генетична предразположеност, тя развила рак на яйчниците и починала едва на 37-годишна възраст през 1958 година. Докато Уотсън и Крик обират лаврите, името на Франклин за съжаление не добива такава популярност. Изследванията й обаче не са престанали да будят интерес и са ни изключително полезни и за настоящия проект.

Снимка номер 51:
Photo_51_x-ray_diffraction_image

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CubeSat Attitude Determination and Control Systems (ADCS)

General conceptual scheme of the ADCS system

adcs-sys

Reference: ADCS

Spaceflight Science – video lectures (short 5-15 min)

Attitude Control System Test Facility (various tests & Helmholtz Cage)

STK cubesat simulation

Micro-Opto-Electro-Mechanical Systems (MOEMS)

Micro-Opto-Electro-Mechanical Systems (MOEMS) is not a special class of Micro-Electro-Mechanical Systems (MEMS) but in fact it is MEMS merged with Micro-optics which involves sensing or manipulating optical signals on a very small size scale using integrated mechanical, optical, and electrical systems. MOEMS includes a wide variety of devices including optical switchoptical cross-connect, tunable VCSELmicrobolometers amongst others. These devices are usually fabricated using micro-optics and standard micromachining technologies using materials like silicon, silicon dioxide, silicon nitride and gallium arsenide.

MOEMS: Merging Multi Technologies[edit]

MOEMS includes two major technologies, MEMS and Micro-optics. Both these two technologies independently involve in batch processing similar to integrated circuits, and micromachining similar to fabrication of microsensor.

MEMS offers inherently device miniaturization and wide applications in sensors and actuators, robotics, accelerometers, microvalves, flow controllers, global positioning systems (GPS) component miniaturization; and a host of other sensors and actuators for applications to space, air, land, and sea vehicles, as well as industrial, biotechnology, and consumer electronics

During 1980s the acronym of MEMS created a fortune for publication, getting government contracts and publicity. DARPA assigned a program manager for this field and significantly soon MEMS is promoted to be the king of the technology. Several high tech journals that were originated were attached to MEMS by supporting miniaturization and low cost manufacturing. Many private companies which did not have sufficient knowledge about MEMS also started jumping on the bandwagon.

Parallel with MEMS developments and even earlier, sensor technology advanced to microsensors and joining with microactuators. Development of microsensors and microactuators were also due to a mother technology of micromachining. Micromachining is the root of everything we have today in high technology. This technology was never credited in history as it deserved. It was commercially used during 1960s in Switzerland, for micromachining[disambiguation neededquartz orders of magnitudes harder than micromachining silicon. MEMS acronym was so powerful during 1980s, that with no choice microsensors and microactuators that included micromachining, all joined MEMS by a soft landing. As a result, the MEMS acronym was more attractive for publicity and even today MEMS, is dominating in microtechnologies without giving credit to its real parents.

During the MEMS era, and before that time frame, Rockwell International was involved in commercial MEMS development under government contracts. During early1980s Rockwell successfully built the first CMOS MEMS high performance and high G accelerometer chip for space applications.[1] The wafer was processed inside Rockwell VLSI lab in Anaheim, CA. This was a breakthrough in MEMS technology, but it did not appear in literature until 1988.

During early 1990s, Rockwell Science Center, through internal research and commercial programs with government sponsors, contributed to the development of micro-optics technology Teamed with MIT/Lincoln-Lab. During 1992, Rockwell applied micro-optics to the system development of several industrial applications, including, microlenses for silicon focal planes,[2] high speed binary microlens in GaAs,[3] antireflection surfaces in silicon,[4] thin film microlens arrays,[5] beam steering device,[6] microlens integration with focal plane arrays,[7] and optical transformer and collimator.[8] Rockwell Science Center also developed refractive microlens technology, including gray scale photolithography.[9]Diffractive microlenses based on binary optic structures are typically fabricated in bulk material by multiple sequential layers of photoresist patterning and reactive ion etching (RIE), to form a multi-step phase profile. This profile approximates the ideal kinoform lens surface. A special staircase process, called binary optics, is used to fabricate diffractive components.

With so many successes in Micro-optics and MEMS, Rockwell researchers who were involved in both MEMS and Micro-optics, initiate development of several of innovative photonics ideas combing both technologies. This was behind the acronym of MOEMS, when both MEMS and Micro-optics were merged in one single IC processing lab.

MOEMS is a promising multi technology for miniaturization of critical optical systems. The acronym is defined of three high tech fields of micro-optics, micromechanics, and microelectronics. MOEMS indirectly could merge in micromachining, microsensors and microactuators if their processes are compatible with integrated circuits.

Merging all these multi technologies, made MOEMS an ideal knowhow for many industrial demonstrations of commercial devices, such as optical switches, digital micromirror devices (DMD), bistable mirrors, laser scanners, optical shutters, and dynamic micromirror displays. All technologies of MOEMS have the potential of batch processing and embossed replication which, again, makes them highly attractive and necessary for commercial applications. MOEMS is an enabling technology for applications that cannot be addressed, using micro-optics alone and is currently playing a significant role in numerous optical applications. The trend toward miniaturization and integration of conventional optical systems will accelerate the adoption of MOEMS technology in commercialization of many industrial components which are today’s most desirable elements of optical communication.

History of MOEMS

REf.: wikipedia.org

RTOS – Real Time Operating System

RTOS – Real Time Operating System

Real-Time Operating System (RTOS) comprises of two components, viz., “Real-Time” and “Operating System”.
An Operating system (OS) is nothing but a collection of system calls or functions which provides an interface between hardware and application programs. It manages the hardware resources of a computer and hosting applications that run on the computer. An OS typically provides multitasking, synchronization, Interrupt and Event Handling, Input/ Output, Inter-task Communication, Timers and Clocks and Memory Management. Core of the OS is the Kernel which is typically a small, highly optimised set of libraries.
Real-time systems are those systems in which the correctness of the system depends not only on the logical result of computation, but also on thetime at which the results are produced.
RTOS is therefore an operating system that supports real-time applications by providing logically correct result within the deadline required.  Basic Structure is similar to regular OS but, in addition, it provides mechanisms to allow real time scheduling of tasks.
Though real-time operating systems may or may not increase the speed of execution, they can provide much more precise and predictable timing characteristics than general-purpose OS.
Real Time Embedded System with RTOS
RTOS is key to many embedded systems and provides a platform to build applications. All embedded systems are not designed with RTOS. Embedded systems with relatively simple/small hardware/code might not require an RTOS. Embedded systems with moderate-to-large software applications require some form of scheduling, and hence RTOS.
DIFFERENCE: RTOS v/s General Purpose OS
·         Determinism – The key difference between general-computing operating systems and real-time operating systems is the “deterministic ” timing behavior in the real-time operating systems.  “Deterministic” timing means that OS consume only known and expected amounts of time. RTOS have their worst case latency defined. Latency is not of a concern for General Purpose OS.
·         Task Scheduling – General purpose operating systems are optimized to run a variety of applications and processes simultaneously, thereby ensuring that all tasks receive at least some processing time. As a consequence, low-priority tasks may have their priority boosted above other higher priority tasks, which the designer may not want. However, RTOS uses priority-based preemptive scheduling, which allows high-priority threads to meet their deadlines consistently. All system calls are deterministic, implying time bounded operation for all operations and ISRs.  This is important for embedded systems where delay could cause a safety hazard. The scheduling in RTOS is time based.  In case of General purpose OS, like Windows/Linux, scheduling is process based.
·         Preemptive kernel – In RTOS, all kernel operations are preemptible
·         Priority Inversion – RTOS have mechanisms to prevent priority inversion
·        Usage – RTOS are typically used for embedded applications, while General Purpose OS are used for Desktop PCs or other generally purpose PCs.
 
RTOS CLASSFICATION
RTOS specifies a known maximum time for each of the operations that it performs. Based upon the degree of tolerance in meeting deadlines, RTOS are classified into following categories
·         Hard real-time: Degree of tolerance for missed deadlines is negligible. A missed deadline can result in catastrophic failure of the system
·         Firm real-time:  Missing a deadly ne might result in an unacceptable quality reduction but may not lead to failure of the complete system
·        Soft real-time:  Deadlines may be missed occasionally, but system doesn’t fail and also, system quality is acceptable
For a life saving device, automatic parachute opening device for skydivers, delay can be fatal. Parachute opening device deploys the parachute at a specific altitude based on various conditions. If it fails to respond in specified time, parachute may not get deployed at all leading to casualty. Similar situation exists during inflation of air bags, used in cars, at the time of accident. If airbags don’t get inflated at appropriate time, it may be fatal for a driver.  So such systems must be hard real time systems, whereas for TV live broadcast, delay can be acceptable. In such cases, soft real time systems can be used.
Important terminologies used in context of real time systemsRTOS2
·         Determinism:   An application is referred to as deterministic if its timing can be guaranteed within a certain margin of error.
·         Jitter:  Timing error of a task over subsequent iterations of a program or loop is referred to as jitter. RTOS are optimized to minimize jitter.

What is MEMS Technology?!?

What is MEMS Technology?

Micro-Electro-Mechanical Systems, or MEMS, is a technology that in its most general form can be defined as miniaturized mechanical and electro-mechanical elements (i.e., devices and structures) that are made using the techniques of microfabrication. The critical physical dimensions of MEMS devices can vary from well below one micron on the lower end of the dimensional spectrum, all the way to several millimeters. Likewise, the types of MEMS devices can vary from relatively simple structures having no moving elements, to extremely complex electromechanical systems with multiple moving elements under the control of integrated microelectronics. The one main criterion of MEMS is that there are at least some elements having some sort of mechanical functionality whether or not these elements can move. The term used to define MEMS varies in different parts of the world. In the United States they are predominantly called MEMS, while in some other parts of the world they are called “Microsystems Technology” or “micromachined devices”.

While the functional elements of MEMS are miniaturized structures, sensors, actuators, and microelectronics, the most notable (and perhaps most interesting) elements are the microsensors and microactuators. Microsensors and microactuators are appropriately categorized as “transducers”, which are defined as devices that convert energy from one form to another. In the case of microsensors, the device typically converts a measured mechanical signal into an electrical signal.

Over the past several decades MEMS researchers and developers have demonstrated an extremely large number of microsensors for almost every possible sensing modality including temperature, pressure, inertial forces, chemical species, magnetic fields, radiation, etc. Remarkably, many of these micromachined sensors have demonstrated performances exceeding those of their macroscale counterparts. That is, the micromachined version of, for example, a pressure transducer, usually outperforms a pressure sensor made using the most precise macroscale level machining techniques. Not only is the performance of MEMS devices exceptional, but their method of production leverages the same batch fabrication techniques used in the integrated circuit industry – which can translate into low per-device production costs, as well as many other benefits. Consequently, it is possible to not only achieve stellar device performance, but to do so at a relatively low cost level. Not surprisingly, silicon based discrete microsensors were quickly commercially exploited and the markets for these devices continue to grow at a rapid rate.

More recently, the MEMS research and development community has demonstrated a number of microactuators including: microvalves for control of gas and liquid flows; optical switches and mirrors to redirect or modulate light beams; independently controlled micromirror arrays for displays, microresonators for a number of different applications, micropumps to develop positive fluid pressures, microflaps to modulate airstreams on airfoils, as well as many others. Surprisingly, even though these microactuators are extremely small, they frequently can cause effects at the macroscale level; that is, these tiny actuators can perform mechanical feats far larger than their size would imply. For example, researchers have placed small microactuators on the leading edge of airfoils of an aircraft and have been able to steer the aircraft using only these microminiaturized devices.


A surface micromachined electro-statically-actuated micromotor fabricated by the MNX. This device is an example of a MEMS-based microactuator.

The real potential of MEMS starts to become fulfilled when these miniaturized sensors, actuators, and structures can all be merged onto a common silicon substrate along with integrated circuits (i.e., microelectronics). While the electronics are fabricated using integrated circuit (IC) process sequences (e.g., CMOS, Bipolar, or BICMOS processes), the micromechanical components are fabricated using compatible “micromachining” processes that selectively etch away parts of the silicon wafer or add new structural layers to form the mechanical and electromechanical devices. It is even more interesting if MEMS can be merged not only with microelectronics, but with other technologies such as photonics, nanotechnology, etc. This is sometimes called “heterogeneous integration.” Clearly, these technologies are filled with numerous commercial market opportunities.

While more complex levels of integration are the future trend of MEMS technology, the present state-of-the-art is more modest and usually involves a single discrete microsensor, a single discrete microactuator, a single microsensor integrated with electronics, a multiplicity of essentially identical microsensors integrated with electronics, a single microactuator integrated with electronics, or a multiplicity of essentially identical microactuators integrated with electronics. Nevertheless, as MEMS fabrication methods advance, the promise is an enormous design freedom wherein any type of microsensor and any type of microactuator can be merged with microelectronics as well as photonics, nanotechnology, etc., onto a single substrate.


A surface micromachined resonator fabricated by the MNX. This device can be used as both a microsensor as well as a microactuator.

This vision of MEMS whereby microsensors, microactuators and microelectronics and other technologies, can be integrated onto a single microchip is expected to be one of the most important technological breakthroughs of the future. This will enable the development of smart products by augmenting the computational ability of microelectronics with the perception and control capabilities of microsensors and microactuators. Microelectronic integrated circuits can be thought of as the “brains” of a system and MEMS augments this decision-making capability with “eyes” and “arms”, to allow microsystems to sense and control the environment. Sensors gather information from the environment through measuring mechanical, thermal, biological, chemical, optical, and magnetic phenomena. The electronics then process the information derived from the sensors and through some decision making capability direct the actuators to respond by moving, positioning, regulating, pumping, and filtering, thereby controlling the environment for some desired outcome or purpose. Furthermore, because MEMS devices are manufactured using batch fabrication techniques, similar to ICs, unprecedented levels of functionality, reliability, and sophistication can be placed on a small silicon chip at a relatively low cost. MEMS technology is extremely diverse and fertile, both in its expected application areas, as well as in how the devices are designed and manufactured. Already, MEMS is revolutionizing many product categories by enabling complete systems-on-a-chip to be realized.

Nanotechnology is the ability to manipulate matter at the atomic or molecular level to make something useful at the nano-dimensional scale. Basically, there are two approaches in implementation: the top-down and the bottom-up. In the top-down approach, devices and structures are made using many of the same techniques as used in MEMS except they are made smaller in size, usually by employing more advanced photolithography and etching methods. The bottom-up approach typically involves deposition, growing, or self-assembly technologies. The advantages of nano-dimensional devices over MEMS involve benefits mostly derived from the scaling laws, which can also present some challenges as well.


An array of sub-micron posts made using top-down nanotechnology fabrication methods.

Some experts believe that nanotechnology promises to: a). allow us to put essentially every atom or molecule in the place and position desired – that is, exact positional control for assembly, b). allow us to make almost any structure or material consistent with the laws of physics that can be specified at the atomic or molecular level; and c). allow us to have manufacturing costs not greatly exceeding the cost of the required raw materials and energy used in fabrication (i.e., massive parallelism).


A colorized image of a scanning-tunneling microscope image of a surface, which is a common imaging technique used in nanotechnology.

Although MEMS and Nanotechnology are sometimes cited as separate and distinct technologies, in reality the distinction between the two is not so clear-cut. In fact, these two technologies are highly dependent on one another. The well-known scanning tunneling-tip microscope (STM) which is used to detect individual atoms and molecules on the nanometer scale is a MEMS device. Similarly the atomic force microscope (AFM) which is used to manipulate the placement and position of individual atoms and molecules on the surface of a substrate is a MEMS device as well. In fact, a variety of MEMS technologies are required in order to interface with the nano-scale domain.

Likewise, many MEMS technologies are becoming dependent on nanotechnologies for successful new products. For example, the crash airbag accelerometers that are manufactured using MEMS technology can have their long-term reliability degraded due to dynamic in-use stiction effects between the proof mass and the substrate. A nanotechnology called Self-Assembled Monolayers (SAM) coatings are now routinely used to treat the surfaces of the moving MEMS elements so as to prevent stiction effects from occurring over the product’s life.

Many experts have concluded that MEMS and nanotechnology are two different labels for what is essentially a technology encompassing highly miniaturized things that cannot be seen with the human eye. Note that a similar broad definition exists in the integrated circuits domain which is frequently referred to as microelectronics technology even though state-of-the-art IC technologies typically have devices with dimensions of tens of nanometers. Whether or not MEMS and nanotechnology are one in the same, it is unquestioned that there are overwhelming mutual dependencies between these two technologies that will only increase in time. Perhaps what is most important are the common benefits afforded by these technologies, including: increased information capabilities; miniaturization of systems; new materials resulting from new science at miniature dimensional scales; and increased functionality and autonomy for systems.

 

Ref. https://www.mems-exchange.org/MEMS/what-is.html

“Четците” за ДНК

Водещи учени казват, че бъдещето на съхранението на информация е в използването на ДНК, и ние от биологичния екип към Cube Sat имаме за цел да развием точно тази идея. Звучи отвлечено и, хм…малко като научна фантастика :). Докато ние все още се чудим на идеята обаче, учени от Харвард още през 2012 са успели да запишат книга от 5,27 мегабита на ДНК и дори да я прочетат след известен период.  Най-много ни привлече идеята за разчитането на информацията, която хипотетично сме записали в молекулата. Идеята е ДНК да премине през така наречените нанопори, които може да са обикновени белтъчни канали от различни порини в мембрана, или да са върху синтетични мембрани (в идеалния случай от графен, но се използват и такива от силициев диоксид или силициев нитрид).

Повече информация можете да откриете на сайта на фирмата, която произвежа четците:

https://www.nanoporetech.com/home

А ето и една схема на принципа на разчитането на ДНК, когато се използват т. нар. биологични нанопори:

nanopore_x616[1]

 

Това е най-доброто видео, което открих във връзка с темата:

 

Ще ви държим в течение за интересните неща на които се натъкваме, може да ви поотегчаваме стабилно понякога, затова приветстваме коментари – кое ви е интересно и искате повече да наблегнем на него, къде сме направили грешки (де да бяхме като полимеразите – 1 грешка на милиард нуклеотиди), и изобщо каквото ви хрумне.